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rms2
01-29-2017, 01:01 PM
Okay, I am somewhat used to dealing with Big Y results that yield "public" SNPs, that is, SNPs that are shared by a fairly large number of men with no apparent connection in genealogical time. But now one of my same-surname matches (109/111) has had the test, submitted his results to Alex Williamson, and has found that we share a string of apparently "private" SNPs unique to our y-dna line.

What is the best course of action in that case?

Here we are on the Big Tree (scroll down and to the right to find us: Stevens 59080 and Stevens 522600):

The Big Tree: R-DF41/S524 (http://www.ytree.net/DisplayTree.php?blockID=7)

Up until yesterday, I was in the same box with Selfe and Samuel, who also belong to our haplotype cluster.

MitchellSince1893
01-29-2017, 02:47 PM
I'm in a similar situation. 40+ SNPS shared between my father and closest match...but different surnames (my line has an NPE) and MRCA is 1000 years ago according to Yfull, and 800 years ago via str method.

Ideas going forward:
1. I worked with FTDNA to get a couple of SNPs added to the appropriate SNP pack test.
2. I requested individual tests from ftdna for these SNPs...no word on that yet.
3. Make a wish list for these SNPs at yseq.net
4. Ask Thomas Krahn to add them to his pertinent L21 branch panel test...or if too recent you could request a personal panel test.
5. Submit both BigY tests to Yfull to get an age estimate. If you already know your MRCA then this will let you know how accurate their dating methodology worked on your branch.

rms2
01-29-2017, 03:00 PM
I'm in a similar situation. 40+ SNPS shared between my father and closest match...but different surnames (my line has an NPE) and MRCA is 1000 years ago according to Yfull, and 800 years ago via str method.

Ideas going forward:
1. I worked with FTDNA to get a couple of SNPs added to the appropriate SNP pack test.
2. I requested individual tests from ftdna for these SNPs...no word on that yet.
3. Make a wish list for these SNPs at yseq.net
4. Ask Thomas Krahn to add them to his pertinent L21 branch panel test...or if too recent you could request a personal panel test.
5. Submit both BigY tests to Yfull to get an age estimate. If you already know your MRCA then this will let you know how accurate their dating methodology worked on your branch.

Thanks! Those are just the sorts of suggestions I was looking for. I wasn't sure any company would agree to test for what are apparently private SNPs.

MitchellSince1893
01-29-2017, 03:48 PM
I'm pretty sure Yseq.net will

rms2
01-29-2017, 03:54 PM
I'm pretty sure Yseq.net will

You mentioned YFull. What is the advantage of paying the $50 for its services? (Honest question: I have no agenda in asking it.)

rms2
01-29-2017, 04:04 PM
The Big Tree is somewhat confusing to me. I see seven SNPs listed in the box on the DF41 Big Tree page that are shared by my 109/111 Stevens match and me. Clicking on the mutation matrix for FGC36975, I count five solid "+" signs that he and I share, but I am the only one with a "+" sign for FGC36983, even though it is listed in the box on the main DF41 page as shared by both of us.

Here is that mutation matrix.

13696

Here is a screen shot of part of the main DF41 Big Tree page showing the box of shared SNPs.

13697

MitchellSince1893
01-29-2017, 04:33 PM
Short Answer: Best answer is to ask Alex directly. But it appears Alex has chosen to display in tree all + +, all ** **, and + pink for your branch


...those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the VCF file. This is particularly true when most men would otherwise show coverage at that particular position.

I remember I had a question on a SNP Alex didn't initially display as shared (I found this SNP via either Yfull or FGC analysis). Alex manually reviewed and added the SNP in question to our shared list.

So it may be that Alex manually reviewed the pink cell SNP and determined it was valid.

As the the inclusion of FGC36977 with the ** and gray cell background. I dunno. Best ask Alex why that was included. Again he may have manually looked at it and determined it was indeed a valid SNP.

rms2
01-29-2017, 04:38 PM
Thanks. I will ask him.

What about YFull? If my Stevens match and I submit our raw data to them, will they give us an estimated tmrca? I suspect our common ancestor was born either around 1776 or around 1750, but I'm not sure.

MitchellSince1893
01-29-2017, 05:12 PM
You mentioned YFull. What is the advantage of paying the $50 for its services? (Honest question: I have no agenda in asking it.)

In my situation, the SNP dating was very important. It may not be in your case.

Other benefits.
Another set of experts with different criteria to analyze your data. As FTDNA, FGC, Alex Williamson, and Yfull all use different criteria in rating the quality of SNPs, I have found it useful to compare between companies. Sometimes a SNP may fall just outside of one company's criteria as valid, but be within another's.

I like the user interface available. I can see details on all my SNPs including the novel ones

Example
ChrY position: 7547230 (+strand)
Reads: 47
Position data: 47T
Weight for T: 1.0
Probability of error: 0.0 (0<->1)
Sample allele: T
Reference (hg19) allele: C
Known SNPs at this position: FGC12384 (C->T) Rating for known SNP 5 stars

They break the novel SNPs down into categories. Best, acceptable, ambiguous, low quality, one reads

You can see your SNP matches...don't expect a lot as their database is not as robust as others. I only see one close match.

Details on SNPs used for age estimation including public and novel SNPs used and not used...and why there were not used.

A y report that shows stats on your BigY bam file size, length of coverage, median depth of coverage, and a tree list of every single SNP you test positive for from A1 to your current terminal branch/block of SNPs

A display of up to 500 STR values...most folks only get about 300 to low 400 STRs that are readable. My father's BigY has 475 STRs of which 406 are readable.
A display of your STR matches...both close and distant.

Display of your STR values compared to the ancestral values

You can browse your raw data by SNP position number

Other stats such as
ChrY BAM file size: 0.51 Gb
Reads (all): 9962312
Mapped reads: 9962312 (100.00%)
Unmapped reads: 0
Length coverage: 13179112 bp (51.37%)
Min depth coverage: 1X
Max depth coverage: 7999X
Mean depth coverage: 66.20X
Median depth coverage: 41X
Length coverage for age: 7269144 bp
No call: 12474454 bp

Known SNPs
SNPs (all): 100571
Positive: 2072 (2.06%)
Negative: 76089 (75.66%)
Ambiguous: 287 (0.29%)
No call: 22082 (21.96%)

STRs
STRs (all): 475
Reliable alleles: 406 (85.47%)
Uncertain alleles: 17 (3.58%)
N/A: 52 (10.95%)

Stats on Novel SNPs
Novel SNPs (all): 45
Best qual: 4 (8.89%) [2 (4.44%) - best; 2 (4.44%) - acceptable]
INDELs: 0
Ambiguous qual: 41 (91.11%)
One read!: 0
Low qual: 0

Mt dna stats
ChrM BAM file size: 431.78 Kb
Length coverage: 16562 bp (99.96%)
Min depth coverage: 2X
Max depth coverage: 3254X
Mean depth coverage: 58.43X
Median depth coverage: 26X
One reading position!: 0
No call: 7 bp

Additional Mt dna info on rcrs and rsrs values

You can also join the appropriate group(s) The L21 group has 385 members in it. A drop in the bucket, but there may be someone in there that's not in the FTDNA project(s). You never know.

For me the $50 was well spent.

MitchellSince1893
01-29-2017, 05:28 PM
Thanks. I will ask him.

What about YFull? If my Stevens match and I submit our raw data to them, will they give us an estimated tmrca? I suspect our common ancestor was born either around 1776 or around 1750, but I'm not sure.

Yes they will. I find using a combination of STR dating and SNP dating useful. In my case, I'm in that "gray area" just outside the genealogical records timeframe.

On my branch, it ranged from 733 to 1247 years before present for the 3 kits on my current terminal branch (average 977 years and 95% CI it's 1500-600 ybp) . When I compare this to http://www.mymcgee.com/tools/yutility111.html I get a 95% probability our MRCA lived 870 years ago. So there is an overlap between the two. As you get beyond this time frame there is a divergence between STR and SNP dating with SNPs giving older dates.

More on this here http://www.anthrogenica.com/showthread.php?9526-Y-DNA-Y-STR-111-Marker-Match-Mismatch-With-Arab-man&p=210149&viewfull=1#post210149

What yfull will do is take a look at both of your individual kit's and come up with age estimates for each and then take the average. They will start from the present (1950) and work back, using the number private SNPs (ones that meet their criteria for use) that neither of you share with each other.

For example. Let's say you have 2 private SNPs and your match has 3 (SNPs not on Alex's tree). They will look at each bam file and make adjustments to the average SNP mutation period. Based on your particular bam file you may have an average of 161 years per SNP mutation. Your match may have 147 (these numbers are just examples). So 2 x 161 would give 322 years based on your kit, and 441 years for your match. They would then take the average of 322 and 441 i.e. 382 years. But you would have a range combined with STR dating to consider as possibilities...it should help get you in the ball park.

rms2
01-29-2017, 08:59 PM
That definitely sounds worthwhile. Thanks!

rms2
01-30-2017, 04:00 PM
Okay, I ordered the YFull thingy just a few minutes ago. We'll see (said the blind man). ;)

ArmandoR1b
01-30-2017, 05:24 PM
Okay, I ordered the YFull thingy just a few minutes ago. We'll see (said the blind man). ;)

Is your match going to order it too?

rms2
01-30-2017, 05:27 PM
Is your match going to order it too?

I believe he is, and another guy in our cluster who has Big Y results will, too.

Osiris
01-30-2017, 06:58 PM
Okay, I ordered the YFull thingy just a few minutes ago. We'll see (said the blind man). ;)
Other fun stuff there is
1. They downloaded lots of genomes from the 1k genomes, Francalacci et al (2013) and others. I loaded myself and my father-in-law there and in both cases have some fairly recent matches in those projects. If I was able to load that data to the Big Tree it would break my most recent large block of SNPs in half.
2. They have groups that you can join. I joined the U152 project. Groups have SNP browsers so I took the novel variants that FTDNA gave me a plugged them into the browser and it became instantly clear which ones were stable and which ones were not.

dp
01-30-2017, 07:17 PM
The Big Tree is somewhat confusing to me. I see seven SNPs listed in the box on the DF41 Big Tree page that are shared by my 109/111 Stevens match and me. Clicking on the mutation matrix for FGC36975, I count five solid "+" signs that he and I share, but I am the only one with a "+" sign for FGC36983, even though it is listed in the box on the main DF41 page as shared by both of us.

Here is that mutation matrix.

13696

Here is a screen shot of part of the main DF41 Big Tree page showing the box of shared SNPs.

13697

Congrats :-)
-dp

rms2
01-30-2017, 09:01 PM
I believe he is, and another guy in our cluster who has Big Y results will, too.

I also emailed the fourth member of my little haplotype cluster project with Big Y results and asked him to consider ordering YFull's service.

YFull sent me an email confirming that they received my BAM file, it has been downloaded, verified, and will be batched. Now I am just waiting for the results.

How long does that usually take?

Oh, my closest same-surname match is trying to order YFull and has asked FTDNA to generate his BAM file, but that is going to take some time apparently. I remember it taking maybe a couple of days, but FTDNA told him it could take up to 2-3 weeks.

gotten
01-30-2017, 09:36 PM
How long does that usually take?

I have three kits on Yfull although the most recent one is almost a year ago:

First one was uploaded on March 29th 2015. First official results and request for payment on April 15th 2015. STRs on May 22nd 2015.
Second kit on March 30th 2016. First results on April 18th 2016. STRs on May 20th 2016.
My most recent kit was uploaded on May 12th 2016. First results were posted on June 18th. The STR results got posted on August 24th.

A genetic relative of mine uploaded a kit on June 3rd 2016, with initial estimates for first results on July 27th and STRs on November 18th (STRs were actually completed on October 14th).

Certain intermediate results and features are available earlier (even without payment) but I don't recall how long they took for each case. Just check every once in a while and click on all the different options.

lgmayka
01-30-2017, 09:41 PM
How long does that usually take?
Usually about a month, but the official due date is probably more like two months. That's only for Y-SNPs. Y-STRs are of much lower priority and may take several months.

Here's a hint: One feature, "Browse Raw Data", is available immediately, even before payment. This is useful if you have an urgent need to check whether you tested positive for a specific SNP. You need to look up the SNP's numeric location to do this--the corresponding symbolic lookup, "Check SNPs", is not available until after analysis and payment.


Oh, my closest same-surname match is trying to order YFull and has asked FTDNA to generate his BAM file, but that is going to take some time apparently. I remember it taking maybe a couple of days, but FTDNA told him it could take up to 2-3 weeks.
FTDNA apparently generates BAM files in batches, roughly once a week--but they sometimes skip a week.

Mikewww
01-31-2017, 03:59 PM
...
What is the best course of action in that case?


I'm in a similar situation. 40+ SNPS shared between my father and closest match...but different surnames (my line has an NPE) and MRCA is 1000 years ago according to Yfull, and 800 years ago via str method.

Ideas going forward:
1. I worked with FTDNA to get a couple of SNPs added to the appropriate SNP pack test.
2. I requested individual tests from ftdna for these SNPs...no word on that yet.
3. Make a wish list for these SNPs at yseq.net
4. Ask Thomas Krahn to add them to his pertinent L21 branch panel test...or if too recent you could request a personal panel test.
5. Submit both BigY tests to Yfull to get an age estimate. If you already know your MRCA then this will let you know how accurate their dating methodology worked on your branch.

I agree with Mitchell's recommendations. I also recommend adding the shared SNPs to the FTDNA haplotree, which is as you know, is already done. The DF41 SNP Pack is due for an update so now is a good time for a revision. There are about 130 SNPs currently so you could 30 without problem and probably get rid of some phylogenetic equivalents that aren't going anywhere (have been thoroughly tested).

dp
01-31-2017, 11:34 PM
Where can I find the rs type id labels for SNPs in R1b, particularly those for U152, DF27, L21, P312 and U106?
I think Ancestry.com is testing Y-DNA SNPs but using the rs ids instead of base pair positions.
dp :-)

gotten
01-31-2017, 11:51 PM
Where can I find the rs type id labels for SNPs in R1b, particularly those for U152, DF27, L21, P312 and U106?

Ybrowse.org has rs type ids in the row with dbSNP149 when you search for a SNP.
Example : here (http://ybrowse.org/gb2/gbrowse/chrY/?start=NaN;stop=NaN;ref=ChrY;width=1024;version=10 0;flip=0;grid=1;id=75b5b255d64b60d6bcd49d891a560a8 2;l=snps%1EDNA%1Eindel%1EdbSNP149%1ESTR%1ECYT%3Aov erview)
You can doublecheck the position/ID in dbSNP https://www.ncbi.nlm.nih.gov/SNP/.

dp
02-01-2017, 12:17 AM
Ybrowse.org has rs type ids in the row with dbSNP149 when you search for a SNP.
Example for U106: here (http://ybrowse.org/gb2/gbrowse/chrY/?start=NaN;stop=NaN;ref=ChrY;width=1024;version=10 0;flip=0;grid=1;id=75b5b255d64b60d6bcd49d891a560a8 2;l=snps%1EDNA%1Eindel%1EdbSNP149%1ESTR%1ECYT%3Aov erview)
You can doublecheck the position/ID in dbSNP https://www.ncbi.nlm.nih.gov/SNP/.
Thanks.
I had some measure of success of searching my relative's Ancestry data file:
P311 => rs9785659 24 18248698 G G
P310 =>rs9786283 24 18907236 C C
U106 =>rs16981293 24 8796078 C C

next question. What are the ancestral allele values so I can make sure C is ancestral and not derived.
didnt find P312, U152, L21, etc.
Maybe I can find out if kit is P310xU106?
dp :-)

ArmandoR1b
02-01-2017, 01:24 AM
Thanks.
I had some measure of success of searching my relative's Ancestry data file:
P311 => rs9785659 24 18248698 G G
P310 =>rs9786283 24 18907236 C C
U106 =>rs16981293 24 8796078 C C

next question. What are the ancestral allele values so I can make sure C is ancestral and not derived.
didnt find P312, U152, L21, etc.
Maybe I can find out if kit is P310xU106?
dp :-)

I prefer to use the CSV file by Ybrowse at http://ybrowse.org/gbrowse2/gff/ because it provides the position, SNP name, ancestral allele, derived allele, longhand ISOGG name and a column with comments.

However, dbSNP also works. It shows the mutation to be C>T so C is ancestral. https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=16981293

What is the reason that you chose a thread on BigY to ask about these things?

dp
02-01-2017, 10:33 PM
I prefer to use the CSV file by Ybrowse at http://ybrowse.org/gbrowse2/gff/ because it provides the position, SNP name, ancestral allele, derived allele, longhand ISOGG name and a column with comments.

However, dbSNP also works. It shows the mutation to be C>T so C is ancestral. https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=16981293

What is the reason that you chose a thread on BigY to ask about these things?
simply because I saw people knowledgeable about Y posting to it.
Thanks for the other link.
@rich prune these posts if you want. I've saved the page. thanks to all.

ArmandoR1b
02-01-2017, 10:44 PM
simply because I saw people knowledgeable about Y posting to it.
Thanks for the other link.
@rich prune these posts if you want. I've saved the page. thanks to all.

I just thought of something. You must have the Ancestry v1 and not the Ancestry v2 file since you couldn't find U152 and L21. They are included in v2 files.

dp
02-02-2017, 10:47 PM
I just thought of something. You must have the Ancestry v1 and not the Ancestry v2 file since you couldn't find U152 and L21. They are included in v2 files.
Yep. I run a surname project on FTDNA, and have an original Ancestry kit that was transferred into FTDNA. I was curious what Y-DNA info I could glean :-)
There was only one branch under P312 that he was tested for, but not U152 or DF27 one of which I think the member is.
Thanks,
dp

rms2
02-03-2017, 11:07 PM
I know everyone here was waiting breathlessly for this news: my closest same-surname match got his BAM file from FTDNA today and submitted it to YFull. :beerchug:

rms2
03-07-2017, 01:06 PM
I submitted my BAM file to YFull on 30 January 2017. I'm still waiting for the results and have been given a prediction of 27 April for them.

As I mentioned before, my closest Stevens match (aside from my second cousin, who matches me 111/111) also submitted his BAM file to YFull, as did a third member of our haplotype cluster.

Anxiously waiting.

lgmayka
03-07-2017, 02:07 PM
I submitted my BAM file to YFull on 30 January 2017. I'm still waiting for the results and have been given a prediction of 27 April for them.
YFull's interface to PayPal has been nonfunctional for several days now. Presumably, YFull does not want to declare any more results complete (and thereby solicit payment) until the PayPal interface is operational again.

We can only presume that behind the scenes, YFull staff are continuing their analysis of BAM file submissions as usual.

rms2
03-07-2017, 02:52 PM
Thanks for that information. I hope they get that working soon.

asquecco
03-07-2017, 06:11 PM
YFull's interface to PayPal has been nonfunctional for several days now. Presumably, YFull does not want to declare any more results complete (and thereby solicit payment) until the PayPal interface is operational again.

We can only presume that behind the scenes, YFull staff are continuing their analysis of BAM file submissions as usual.

They keep on working.
I'm monitoring a couple of still pending BAM files I submitted in January/February and in the last days they were given a subclade assignment.
Also checking "Statistics/Novel SNPs" I saw yesterday they changed the figures for both.
The issue probably is the calculation overloadingg due to a lot of "new" BAM files you can see in quite every branch of the YTree.

lgmayka
03-07-2017, 09:01 PM
YFull's interface to PayPal has been nonfunctional for several days now.
The YFull-to-PayPal interface is working again. I just paid the fee for YF08472.

rms2
03-08-2017, 12:28 AM
They keep on working.
I'm monitoring a couple of still pending BAM files I submitted in January/February and in the last days they were given a subclade assignment.
Also checking "Statistics/Novel SNPs" I saw yesterday they changed the figures for both.
The issue probably is the calculation overloadingg due to a lot of "new" BAM files you can see in quite every branch of the YTree.

They've updated my predicted results date from 27 April to 16 April. That is something at least.

asquecco
03-08-2017, 07:16 PM
The YFull-to-PayPal interface is working again. I just paid the fee for YF08472.

Same for me. But for the released kit the "SNPs/Age Estimation" tab does not work (it's empty).

lgmayka
03-08-2017, 08:01 PM
Same for me. But for the released kit the "SNPs/Age Estimation" tab does not work (it's empty).
For a newly analyzed YFull account, that tab may not work until the next release of their haplotree.

JMcB
03-08-2017, 08:09 PM
For a newly analyzed YFull account, that tab may not work until the next release of their haplotree.

Yes, that's the way it worked for me last month. The age estimation did not kick in until they updated their tree, which they try to do every month.

rms2
03-08-2017, 09:23 PM
They've updated my predicted results date from 27 April to 16 April. That is something at least.

I just looked at my account again, and now the predicted date for the results is 08 April. Very good! At this rate my results should be out in just a few more days.

rms2
03-08-2017, 11:59 PM
I see my YFull ID number on YFull's tree under CTS2501, but it is hazy and not in sharp focus, which I guess is indicative that the analysis is not yet done. At least it's there, which means things are progressing. B)

lgmayka
03-09-2017, 12:16 AM
I see my YFull ID number on YFull's tree under CTS2501, but it is hazy and not in sharp focus, which I guess is indicative that the analysis is not yet done. At least it's there, which means things are progressing. B)
YFull has completed analysis as far as YF08518 (https://www.yfull.com/tree/R-L644/), as far as I can see.

MitchellSince1893
03-09-2017, 01:13 AM
Looks like you might get in right before the new version comes out. Hopefully so as it would save you an agonizing month of waiting for the next update. If you haven't done so, join the Yfull L21 group once you are able (may have to wait until results are fully analyzed)

JMcB
03-09-2017, 01:16 AM
I see my YFull ID number on YFull's tree under CTS2501, but it is hazy and not in sharp focus, which I guess is indicative that the analysis is not yet done. At least it's there, which means things are progressing. B)

If you know it, don't forget to put in your ancestor's country of origin. It will show up on the tree right next to your number.

14415

rms2
03-09-2017, 09:18 AM
YFull has completed analysis as far as YF08518 (https://www.yfull.com/tree/R-L644/), as far as I can see.

Thanks. I am YF08577, so I'm not too far back in the queue. ☺

rms2
03-09-2017, 09:20 AM
If you know it, don't forget to put in your ancestor's country of origin. It will show up on the tree right next to your number.

14415

I am pretty confident it's Wales, but I can't prove it yet.

JMcB
03-09-2017, 05:41 PM
I am pretty confident it's Wales, but I can't prove it yet.

For the most part, I'm in the same boat. I know my ancestor came from Scotland and I'm pretty sure he was from Galloway but I can't prove the latter. You could always put down Great Britain if you're unsure about Wales

Do you know by chance if you're positive for all of the SNPs contained within CTS2501? The reason I ask, is because the way they've listed you (separated out), is the same way they listed me right before I split the I-L234 branch. Maybe you and your cousin are forming a new branch. On the other hand, I may be wrong about that. Perhaps, Igmayka knows.

rms2
03-09-2017, 06:08 PM
That's possible. Alex Williamson never said anything about it, so I'm not sure. I haven't checked on all those CTS2501 level SNPs.

I'm about 99% sure my immigrant ancestor came from Wales, but I can't prove it, and I don't yet know who my immigrant ancestor was.

rms2
03-09-2017, 06:34 PM
. . .

Do you know by chance if you're positive for all of the SNPs contained within CTS2501? The reason I ask, is because the way they've listed you (separated out), is the same way they listed me right before I split the I-L234 branch. Maybe you and your cousin are forming a new branch. On the other hand, I may be wrong about that. Perhaps, Igmayka knows.

I was just looking at the YFull tree again and thinking about what you wrote, and that sure makes sense. My second cousin and another member of our cluster ordered YFull at around the same time I did, but I don't see any other new ID numbers in the same zone as mine. Maybe they are just not as far along in the analysis as I am.

JMcB
03-09-2017, 06:36 PM
That's possible. Alex Williamson never said anything about it, so I'm not sure. I haven't checked on all those CTS2501 level SNPs.

I'm about 99% sure my immigrant ancestor came from Wales, but I can't prove it, and I don't yet know who my immigrant ancestor was.

Well, we'll probably know soon enough. If I remember correctly, they updated their last tree on February 11th and they try to do it every month. So it may be right around the corner.

Good luck, I hope you soon find out who he was and when he came here.

Are you still working with the genealogist?

rms2
03-09-2017, 11:34 PM
Well, we'll probably know soon enough. If I remember correctly, they updated their last tree on February 11th and they try to do it every month. So it may be right around the corner.

Good luck, I hope you soon find out who he was and when he came here.

Are you still working with the genealogist?

Yes. The Ancestry genealogists have us in their queue. They were supposed to begin work on our line in April, but now it's been postponed until May.

rms2
03-09-2017, 11:41 PM
I was just looking at the YFull tree again and thinking about what you wrote, and that sure makes sense. My second cousin and another member of our cluster ordered YFull at around the same time I did, but I don't see any other new ID numbers in the same zone as mine. Maybe they are just not as far along in the analysis as I am.

Oh, I misspoke above when I said my second cousin ordered YFull. He hasn't ordered it. A very close match (109/111) with my surname ordered it. He's close enough on the y-dna line to be a second cousin, but I think he's a bit more distant than that.

Right now I am waiting for YFull, waiting for my wife's Family Finder results, and waiting for the big Bell Beaker bonanza. I am really impatient. It would be nice to get at least one of those soon to ease the pain of waiting for the others.

rms2
03-09-2017, 11:46 PM
They've updated my predicted results date from 27 April to 16 April. That is something at least.


I just looked at my account again, and now the predicted date for the results is 08 April. Very good! At this rate my results should be out in just a few more days.

Hey! Now they've got my predicted results date down to 04 April! Steady progress! Outstanding! B)

lgmayka
03-10-2017, 12:21 AM
Steady progress!
YF08525 (https://yfull.com/tree/R-FGC35930/)is now complete.

JMcB
03-10-2017, 01:08 AM
Yes. The Ancestry genealogists have us in their queue. They were supposed to begin work on our line in April, but now it's been postponed until May.

I'm looking forward to hearing how they do for you. I've also thought about taking the same route but I have too many expenses at the moment, so it'll have to wait.

rms2
03-10-2017, 09:04 PM
Now they have my predicted results date set at 03 April. Each day things get a little better. B)

As for what we were discussing earlier about my position on YFull's tree for now, I just found out at least one of those new IDs below CTS2501* belongs to my 109/111 Stevens match, who is also my closest Big Y match and who shares my position on Alex Williamson's Big Tree. I suspect the other new ID there might be that of another member of our haplotype cluster, who is also on Alex's Big Tree but who does not share the SNPs that thus far I share only with my 109/111 Stevens match.

So, I don't know what is going on.

lgmayka
03-11-2017, 07:42 PM
YF08525 (https://yfull.com/tree/R-FGC35930/)is now complete.
YF08572 (https://yfull.com/tree/R-A5411/) is now complete.

Please understand that any changes in the tree itself (new subclade, splitting of a clade) will not be visible until the next version of the tree. However, one can often guess what will happen based on unusual entries on the "Hg and SNPs" tab of the YFull account. For example, these three new SNP entries probably herald a new subclade under N-Y13982 (https://yfull.com/tree/N-Y13982/):


Y31236 level N-Y13982 terminal ***** +
Y31235 level N-Y13982 terminal **** +
Y31805 level N-Y13982 terminal **** +

rms2
03-11-2017, 08:19 PM
YF08572 (https://yfull.com/tree/R-A5411/) is now complete.

Please understand that any changes in the tree itself (new subclade, splitting of a clade) will not be visible until the next version of the tree. However, one can often guess what will happen based on unusual entries on the "Hg and SNPs" tab of the YFull account. For example, these three new SNP entries probably herald a new subclade under N-Y13982 (https://yfull.com/tree/N-Y13982/):


Y31236 level N-Y13982 terminal ***** +
Y31235 level N-Y13982 terminal **** +
Y31805 level N-Y13982 terminal **** +


Thanks!

I just checked, and they've moved me up to a predicted results date of 31 March. The way things are going, I think my results will come in earlier than that: maybe sometime this coming week. That would be nice.

asquecco
03-11-2017, 08:36 PM
YF08572 (https://yfull.com/tree/R-A5411/) is now complete.

Please understand that any changes in the tree itself (new subclade, splitting of a clade) will not be visible until the next version of the tree. However, one can often guess what will happen based on unusual entries on the "Hg and SNPs" tab of the YFull account. For example, these three new SNP entries probably herald a new subclade under N-Y13982 (https://yfull.com/tree/N-Y13982/):


Y31236 level N-Y13982 terminal ***** +
Y31235 level N-Y13982 terminal **** +
Y31805 level N-Y13982 terminal **** +


It seems YFull, based on the analysis of new kits, revised the terminal SNP of 2 of my old kits.
But they are both ancestral for the reported new terminal SNP. Actually this SNP seems to have a position just before a DEL reported for both kits.
Could it be a good explanation for that?
Adriano

asquecco
03-11-2017, 09:26 PM
It seems YFull, based on the analysis of new kits, revised the terminal SNP of 2 of my old kits.
But they are both ancestral for the reported new terminal SNP. Actually this SNP seems to have a position just before a DEL reported for both kits.
Could it be a good explanation for that?
Adriano

Yes, it is. I found the answer here:
https://www.yfull.com/snp-list/
Hope YFull will not use this terminal SNP to create a new subclade because my BIG Y kit have the same DEL but starting 1 position after the DEL reported by my FGC kit and another BIG Y kit, so for this reason my BIG Y kit has a different terminal SNP.
Sorry for the OT.
Adriano

JMcB
03-11-2017, 10:12 PM
Now they have my predicted results date set at 03 April. Each day things get a little better. B)

As for what we were discussing earlier about my position on YFull's tree for now, I just found out at least one of those new IDs below CTS2501* belongs to my 109/111 Stevens match, who is also my closest Big Y match and who shares my position on Alex Williamson's Big Tree. I suspect the other new ID there might be that of another member of our haplotype cluster, who is also on Alex's Big Tree but who does not share the SNPs that thus far I share only with my 109/111 Stevens match.

So, I don't know what is going on.

Have you checked how FTDNA has placed you on your haplogroup tree?

In my case, they split me out of I-L234 right away because I was positive for ten of the SNPs in that branch but negative for L234. And because they have more information (results) than YFull, they were able to divide up the L234 branch more finely than YFull eventually did.

You can also see which SNPs they have you as positve for under CTS2501 and compare it to the SNPs YFull lists as being within CTS2501. If your case is like mine, you may be positive for many of the SNPs within CTS2501, while being negative for CTS2501 itself, which would split the branch. But if FTDNA's haplotree shows you as positive for CTS2501 than I would imagine you won't and something else is going on.

rms2
03-12-2017, 01:09 AM
Have you checked how FTDNA has placed you on your haplogroup tree?

In my case, they split me out of I-L234 right away because I was positive for ten of the SNPs in that branch but negative for L234. And because they have more information (results) than YFull, they were able to divide up the L234 branch more finely than YFull eventually did.

You can also see which SNPs they have you as positve for under CTS2501 and compare it to the SNPs YFull lists as being within CTS2501. If your case is like mine, you may be positive for many of the SNPs within CTS2501, while being negative for CTS2501 itself, which would split the branch. But if FTDNA's haplotree shows you as positive for CTS2501 than I would imagine you won't and something else is going on.

Apparently FTDNA is having problems with Haplotree & SNPs pages right now, or at least with mine, because it won't load and the "Internal Server Error" message pops up.

Anyway, my YFull results are in. I just paid, and I'm still trying to figure things out.

If I am reading the YReport correctly, I have no calls at two of the CTS2501 SNPs: Y2369 • FGC5564 and Y2372 • FGC8001. That must be the reason for putting me where they presently have me. I'm not negative for those; I have no calls there.

rms2
03-12-2017, 02:03 AM
I think once YFull finishes their analysis of my two close matches, they will have no trouble placing me in the right spot when they update their tree.

JMcB
03-12-2017, 03:23 AM
Apparently FTDNA is having problems with Haplotree & SNPs pages right now, or at least with mine, because it won't load and the "Internal Server Error" message pops up.

Anyway, my YFull results are in. I just paid, and I'm still trying to figure things out.

If I am reading the YReport correctly, I have no calls at two of the CTS2501 SNPs: Y2369 FGC5564 and Y2372 FGC8001. That must be the reason for putting me where they presently have me. I'm not negative for those; I have no calls there.

Well, I'm glad to hear your results are in and it looks like they had you where you were for some other reason. Fortunately, your results came in before they updated their tree, so you shouldn't have to wait too long to see the results.

rms2
03-12-2017, 01:49 PM
I'll be glad when the YFull analysis of my two closest Big Y matches is finished, as well. I wish the Big Y would come down in price to around 200 bucks so I could talk some more of my haplotype neighbors into it and into the YFull analysis.

JMcB
03-12-2017, 02:17 PM
I'll be glad when the YFull analysis of my two closest Big Y matches are finished, as well. I wish the Big Y would come down in price to around 200 bucks so I could talk some more of my haplotype neighbors into it and into the YFull analysis.

Yeah, I agree! I had to cobble together a sale, a coupon and a year and a half worth of credit card points just to get it down to $280. And to be honest, if it hadn't been for my Z140 administrator, I wouldn't have learned very much from it either but thankfully, he was able to give me some very useful information. So unless you have someone to guide you through it, it's a bit of a hard sell.

rms2
03-12-2017, 02:52 PM
Yeah, I agree! I had to cobble together a sale, a coupon and a year and a half worth of credit card points just to get it down to $280. And to be honest, if it hadn't been for my Z140 administrator, I wouldn't have learned very much from it either but thankfully, he was able to give me some very useful information. So unless you have someone to guide you through it, it's a bit of a hard sell.

I'm lucky my 109/111 Stevens match is really enthusiastic. I first emailed him via Ancestry last summer about the probability of our being related based on inconclusive paper trail stuff. Since then he has caught fire, especially once he saw via our 109/111 match that we are related and that we might have a chance to break through our genealogical brick wall at last.

rms2
03-12-2017, 04:17 PM
Apparently YFull already has in its database the group of SNPs I share thus far only with my 109/111 Stevens match and has them as known SNPs under the FGC prefix. When I search for them on the "Check SNPs" page, I come back positive for them. These are the SNPs that Alex Williamson turned up in his analysis.

rms2
03-12-2017, 06:13 PM
I see they have gotten as far as YF08614. That's just a few away from my Stevens match. It wouldn't surprise me if his results came in this evening or tomorrow. :beerchug:

lgmayka
03-13-2017, 12:03 AM
I see they have gotten as far as YF08614. That's just a few away from my Stevens match.
Analysis of YF08619 is complete, I see.

On the "Hg and SNPs" page of your YFull account, do you see your clan's FGC SNP names? Are they marked as "Terminal"?

On your "Novel SNPs" page, do you have any listed as "Best quality" or "Acceptable quality"?

rms2
03-13-2017, 12:52 AM
Analysis of YF08619 is complete, I see.

On the "Hg and SNPs" page of your YFull account, do you see your clan's FGC SNP names? Are they marked as "Terminal"?

On your "Novel SNPs" page, do you have any listed as "Best quality" or "Acceptable quality"?

Here's what they have at the top of my Hg and SNPs page:

Y-Haplogroup: R-CTS2501
Hg variants: R-CTS2501*
Terminal SNPs: CTS2501/S836 • DF41/S524/CTS6581 • FGC8000/Y2370 • Y2368/FGC7999 • Y2369/FGC5564 • Y2372/FGC8001 • Y2373/S839/SK2221 • Y2374/FGC7998

I have 4 novel SNPs of acceptable quality, none of best quality, but it looks like the new SNPs I got via Alex Williamson's analysis were already added to YFull's database, so those don't show up as novel for me.

14510

So far, I still have no matches on my SNP Matches page, even though the YFull analysis of my closest Big Y match is done. Maybe it will take a little more time for him to show up there.

rms2
03-13-2017, 01:06 AM
I see that FGC8000/Y2370 and Y2368/FGC7999 are not on the CTS2501 level on the Y Tree.

The others I have listed at the top of my HG and SNPs page as "Terminal SNPs" are all on the CTS2501 level.

rms2
03-13-2017, 01:31 AM
The long list of my SNPs on the HG and SNPs page says FGC8000/Y2370 and Y2368/FGC7999 are on the CTS2501 level, but they don't appear listed with CTS2501 on the Y Tree.

I see I am positive for FGC36974, which was one of the SNPs found by Alex Williamson in my BAM file and in the BAM file of my 109/111 Stevens match. It is listed by FTDNA as my terminal SNP. The others are there, as well, as are the BY series SNPs, like BY166, common to my haplotype cluster.

I'm guessing it takes YFull a little time to catch up with matches and the actual set of terminal SNPs.

MitchellSince1893
03-13-2017, 03:47 AM
The long list of my SNPs on the HG and SNPs page says FGC8000/Y2370 and Y2368/FGC7999 are on the CTS2501 level, but they don't appear listed with CTS2501 on the Y Tree.

I see I am positive for FGC36974, which was one of the SNPs found by Alex Williamson in my BAM file and in the BAM file of my 109/111 Stevens match. It is listed by FTDNA as my terminal SNP. The others are there, as well, as are the BY series SNPs, like BY166, common to my haplotype cluster.

I'm guessing it takes YFull a little time to catch up with matches and the actual set of terminal SNPs.

IIRC there was a delay for me on some features. A lot of this updates once the new tree version comes out.

lgmayka
03-13-2017, 04:41 AM
I see I am positive for FGC36974, which was one of the SNPs found by Alex Williamson in my BAM file and in the BAM file of my 109/111 Stevens match. It is listed by FTDNA as my terminal SNP. The others are there, as well, as are the BY series SNPs, like BY166, common to my haplotype cluster.
So it sounds like everything is there. It's all waiting for publication of the next version of the haplotree.

rms2
03-13-2017, 05:26 PM
I took a look this morning at my SNP Matches page. Still no matches, even though I know there should be at least one. I guess that may not show up until the tree update.

I understand that YFull does not show matches on SNPs older than 2500 ybp, which is cool.

rms2
03-14-2017, 01:25 AM
I have been told by someone who is pretty knowledgeable about YFull that my SNP matches probably won't show up until the new 5.03 version of the tree comes out, or possibly a few days before that. Over on the YFull Facebook group Vadim Urasin said he is hoping for early April for version 5.03.

JMcB
03-14-2017, 02:49 AM
I have been told by someone who is pretty knowledgeable about YFull that my SNP matches probably won't show up until the new 5.03 version of the tree comes out, or possibly a few days before that. Over on the YFull Facebook group Vadim Urasin said he is hoping for early April for version 5.03.

That sounds about right. I can't remember about the SNP matches but I was very interested in their Age Estimation and it didn't post until after they updated their tree. They also kept my terminal Haplogroup as I-L234 (even though I was negative for L234) until their new tree came online and they split me out of that branch. So I think a lot hinges on that.

Although, I was hoping their new tree would arrive earlier but c'est la vie.

rms2
03-14-2017, 05:15 PM
I've got to say I really like YFull's features. The HG and SNPs page is really nice and easy to survey. I'll like YFull even better when my SNP matches start showing up and they get me into the right spot on their tree.

rms2
03-16-2017, 11:21 PM
A third member of my haplotype cluster, also one of my closest Big Y matches, got his YFull results today. B)

I also heard from another one of my Stevens matches (108/111), and it looks like he is going to order the Big Y.

JMcB
03-16-2017, 11:47 PM
A third member of my haplotype cluster, also one of my closest Big Y matches, got his YFull results today. B)

I also heard from another one of my Stevens matches (108/111), and it looks like he is going to order the Big Y.

You're on a roll!

rms2
03-17-2017, 10:52 PM
Now I'm waiting for YFull Tree version 5.03 to hit the fan. That's when things will become fun and YFull will earn the 49 bucks apiece we paid.

rms2
03-20-2017, 03:45 PM
Another of my close same-surname matches (108/111) has ordered the Big Y. He intends to get YFull's service once he gets his results.

lgmayka
03-20-2017, 11:23 PM
Now I'm waiting for YFull Tree version 5.03 to hit the fan. That's when things will become fun and YFull will earn the 49 bucks apiece we paid.
YFull has now completed analysis of YF09010 (https://yfull.com/tree/R-A6077*/). As far as I can tell, that is the last of the entries that were awaiting analysis during this iteration. (The next iteration, with later sequence numbers, is not yet on the tree at all.) If I recall correctly, the last of the previous iteration was near YF08270, so this iteration was enormous--over 600 new entries.

YFull now has to make any necessary structural changes to the tree--adding subclades, splitting levels, etc.

rms2
03-21-2017, 12:38 AM
YFull has now completed analysis of YF09010 (https://yfull.com/tree/R-A6077*/). As far as I can tell, that is the last of the entries that were awaiting analysis during this iteration. (The next iteration, with later sequence numbers, is not yet on the tree at all.) If I recall correctly, the last of the previous iteration was near YF08270, so this iteration was enormous--over 600 new entries.

YFull now has to make any necessary structural changes to the tree--adding subclades, splitting levels, etc.

So, is that a sign that they are about to update their tree to version 5.03? If so, how long does that usually take?

MitchellSince1893
03-21-2017, 12:56 AM
So, is that a sign that they are about to update their tree to version 5.03? If so, how long does that usually take?

On facebook yfull page on 13 March, Vadim Urasin, cofounder of Yfull says he hopes to release 5.03 in early April.

I will have a new BigY test on my terminal branch to add for 5.04

rms2
03-21-2017, 11:26 AM
On facebook yfull page on 13 March, Vadim Urasin, cofounder of Yfull says he hopes to release 5.03 in early April.

I will have a new BigY test on my terminal branch to add for 5.04

I remember seeing that. I was just wondering if a more definite date could be guessed at.

lgmayka
03-21-2017, 08:13 PM
I remember seeing that. I was just wondering if a more definite date could be guessed at.
The difficulty in estimating completion of the new tree is that I don't believe I've ever seen an iteration with nearly so many new entries--roughly 640, if I recall correctly. That will probably force plenty of new subclades and some level splitting.

Dubhthach
03-22-2017, 12:17 PM
640 new results now that's impressive! obviously knock on effect from the Christmas sale.

Mikewww
03-22-2017, 03:16 PM
The difficulty in estimating completion of the new tree is that I don't believe I've ever seen an iteration with nearly so many new entries--roughly 640, if I recall correctly. That will probably force plenty of new subclades and some level splitting.
I wonder if the slow downs on the Big Tree are pushing more people over to YFull? I keep hearing that Dr. Iain McDonald's Age estimation methods will be implemented across all of the Big Tree soon, which has huge P312 bent to it and is free, at least currently. However, there is a large backlog awaiting to be finalized on the Big Tree.

I don't know if people understand, but YFull is only looking at the BAM file information whereas the Big Tree looks mostly at the VCF file information. The BAM files have the ultimate detail. Each serve their purpose but there is overlap in that they both generate NGS based trees.

rms2
04-04-2017, 10:52 PM
Last Thursday, 30 March 2017, over on the Facebook YFull group, Vladimir Semargl estimated that Version 5.03 of the YFull Tree would be out in 7-10 days, in his own words, "Maybe a little earlier", so possibly this coming Thursday, 06 April, or even tomorrow, Wednesday, 05 April.

Here is his original post on the subject.



Statistics for the next version 5.03 of our Y-Tree (coming soon):
will be added 3190 SNPs, 670 subclades
by haplogroups:
A00: 1 SNP
A0: 1 SNP
A1b1: 2 SNPs
B: 22 SNPs, 1 subclade
E: 419 SNPs, 63 subclades
C: 4 SNPs, 2 subclades
G: 144 SNPs, 21 subclades
H: 2 SNPs
I1: 328 SNPs, 84 subclades
I2: 194 SNPs, 60 subclades
J1: 149 SNPs, 55 subclades
J2: 317 SNPs, 51 subclades
L: 131 SNPs, 9 subclades
T: 97 SNPs, 9 subclades
M: 1 SNP
Q: 69 SNPs, 3 subclades
R1a: 88 SNPs, 59 subclades
R1b: 1052 SNPs, 201 subclades
R2: 4 SNPs, 6 subclades
N: 73 SNPs, 37 subclades
O: 93 SNPs, 9 subclades
We have used information from samples until YF09010

Mikewww
04-04-2017, 11:08 PM
Last Thursday, 30 March 2017, over on the Facebook YFull group, Vladimir Semargl estimated that Version 5.03 of the YFull Tree would be out in 7-10 days, in his own words, "Maybe a little earlier", so possibly this coming Thursday, 06 April, or even tomorrow, Wednesday, 05 April.

Here is his original post on the subject.

....
"R1b: 1052 SNPs, 201 subclades"

They are still lagging. They'll never come close to a full cross-testing platform tree like ISOGG's (unless it cripples itself) or FTDNA's.

We are now seeing the numbers of Specialized SNP Pack results surpass the Big Y results down at the subclade (i.e. R1b-L513, etc.) level. I'm not counting the R1b-Backbone Pack as there has always been a ton of those and they don't refine branching on the tree, just individual placement.

Just for L21 we see that ISOGG has 449 distinct branches. This is double the number of 201 that YFull has for all of R1b. The FTDNA haplotree has 1,664 branches for just L21 as of last weekend.

I've got a feeling YFull will feel a squeeze in the future unless they come up with some new services, perhaps WGS related.

If the lag in Big Tree placements is really just the preparation for Big Tree v2 then YFull will have pretty much lost R1b. That's too bad as there is a need for a purist NGS BAM assessment. They have turned up new branching that isn't seen in Big Tree since they dig under the VCF files.

At the same time, we've got an academic (Dr. Behar, right?) who will undertake some kind of purist NGS BAM experimental tree too with access to all of FTDNA's data.

rms2
04-04-2017, 11:10 PM
I got the impression that those were the numbers added in Version 5.03 rather than absolute totals.

lgmayka
04-04-2017, 11:25 PM
This is double the number of 201 that YFull has for all of R1b.
:lol: 201 is the number of subclades added in this iteration, not the total number.


I've got a feeling YFull will feel a squeeze in the future unless they come up with some new services, perhaps WGS related.
I don't see any real competition for what YFull provides (I might wish there were), except perhaps in R1b-L151. You are correct that within R1b-L151, it's difficult to compete with $0, except perhaps on the privacy issue. (Many customers are unwilling to post their raw data to a public web site, which is essentially what a Yahoo group is.)


At the same time, we've got an academic (Dr. Behar, right?) who will undertake some kind of purist NGS BAM experimental tree too with access to all of FTDNA's data.
I don't think he can do that legally. In order to publish, he needs to get explicit consent from each customer. Only a fraction of customers ever actually sign an academic release form.

Besides, we all know that publishing an academic paper typically takes several years.

Mikewww
04-05-2017, 12:38 AM
I got the impression that those were the numbers added in Version 5.03 rather than absolute totals.
Good that makes more sense.

I do know a little more about what's going on with Big Y updates and also with Dr Behar.

There will need to be some adjustments. It is not a competition thing directly but there will be some natural fallout.

lgmayka
04-05-2017, 04:24 AM
I do know a little more about what's going on with Big Y updates and also with Dr Behar.
I'm sure Dr. Behar could generate a haplotree from FTDNA data, and FTDNA could then incorporate that tree into their commercial web site, classifications, etc. That would be great!

But I don't see how Dr. Behar can publish an academic paper divorced from the data on which it is based; and he cannot publish customer data without explicit consent. Vague handwaving ("By using this web site, you agree...") may be good enough for commercial legality but does not meet academic standards.

Mikewww
04-05-2017, 07:19 PM
They are still lagging. They'll never come close to a full cross-testing platform tree like ISOGG's (unless it cripples itself) or FTDNA's.

We are now seeing the numbers of Specialized SNP Pack results surpass the Big Y results down at the subclade (i.e. R1b-L513, etc.) level. I'm not counting the R1b-Backbone Pack as there has always been a ton of those and they don't refine branching on the tree, just individual placement.

Just for L21 we see that ISOGG has 449 distinct branches. [delete incorrect statement from prior post]. The FTDNA haplotree has 1,664 branches for just L21 as of last weekend.

I've got a feeling YFull will feel a squeeze in the future unless they come up with some new services, perhaps WGS related.

If the lag in Big Tree placements is really just the preparation for Big Tree v2 then YFull will have pretty much lost R1b. That's too bad as there is a need for a purist NGS BAM assessment. They have turned up new branching that isn't seen in Big Tree since they dig under the VCF files.

At the same time, we've got an academic (Dr. Behar, right?) who will undertake some kind of purist NGS BAM experimental tree too with access to all of FTDNA's data.

I just downloaded the YFull tree for R-L21 and sorted out to distinct branches. The number of subclades YFull has for L21 is 418.

So it is

FTDNA 1,664
ISOGG 449
YFull 418

I think the biggest news here is that ISOGG has nearly fallen behind YFull even though ISOGG accepts cross-test platform submissions (i.e Sanger Sequenced results.)

I am not going to try to count Big Tree branches but I believe it comes in between FTDNA and YFull.

rms2
04-09-2017, 12:32 PM
YFull's new tree, Version 5.03, is up.

Here's the R1b part:

https://www.yfull.com/tree/R1b/

rms2
04-15-2017, 04:46 PM
A 108/111 STR match of mine with my surname received his Big Y results a couple of days ago. He has requested a link to his BAM file from FTDNA so he can share it with YFull and Alex Williamson without actually having to download it on his computer. As soon as he gets it, he plans to submit it to YFull.

When do we expect the next update to YFull's tree? June? July?

lgmayka
04-15-2017, 05:58 PM
When do we expect the next update to YFull's tree? June? July?
The most recent (still grayed-out) addition to YFull's tree seems to be YF09312 (https://yfull.com/tree/R-A14635/). If I recall correctly, the most recent in the last iteration was YF09010. So, this new iteration will add about 300 entries--less than half the extraordinary number of new entries last time (about 640).

Version 5.03 was released on April 9, version 5.02 on February 11. Thus, 640 new entries required less than 2 months of calendar time. We can therefore hope that the 300 new entries this time will be completed within a month--i.e., by May 9. No promises, of course. :biggrin1:

rms2
04-15-2017, 07:37 PM
The most recent (still grayed-out) addition to YFull's tree seems to be YF09312 (https://yfull.com/tree/R-A14635/). If I recall correctly, the most recent in the last iteration was YF09010. So, this new iteration will add about 300 entries--less than half the extraordinary number of new entries last time (about 640).

Version 5.03 was released on April 9, version 5.02 on February 11. Thus, 640 new entries required less than 2 months of calendar time. We can therefore hope that the 300 new entries this time will be completed within a month--i.e., by May 9. No promises, of course. :biggrin1:

Thanks. Excellent. The $49 I spent with YFull is just about the best $49 I ever spent. I should have done it long ago.

My 108/111 Stevens match, btw, is derived for FGC36974, which is what YFull has designated as my terminal SNP (and the terminal SNP of my 109/111 Stevens match). B)

MitchellSince1893
04-15-2017, 09:36 PM
Thanks. Excellent. The $49 I spent with YFull is just about the best $49 I ever spent. I should have done it long ago.

My 108/111 Stevens match, btw, is derived for FGC36974, which is what YFull has designated as my terminal SNP (and the terminal SNP of my 109/111 Stevens match). B)

That's a relief as I was encouraging you to do it.

rms2
04-15-2017, 09:38 PM
That's a relief as I was encouraging you to do it.

Yep. You were right. Thanks!

MitchellSince1893
04-16-2017, 01:01 AM
The most recent (still grayed-out) addition to YFull's tree seems to be YF09312 (https://yfull.com/tree/R-A14635/). If I recall correctly, the most recent in the last iteration was YF09010. So, this new iteration will add about 300 entries--less than half the extraordinary number of new entries last time (about 640).

Version 5.03 was released on April 9, version 5.02 on February 11. Thus, 640 new entries required less than 2 months of calendar time. We can therefore hope that the 300 new entries this time will be completed within a month--i.e., by May 9. No promises, of course. :biggrin1:

My branch has YF09234. Due date was 5/28/2017. Now it's 6/11/2017.

rms2
04-16-2017, 02:11 PM
I have a question. A second cousin who is a 111/111 STR match for me is considering ordering the Big Y. The obvious advantage I can see in his doing that is that we know our exact tmrca: 88 years (using 1950 as the present). That takes us back to our most recent common ancestor, our y-dna great grandfather, who was born 23 October 1862.

I am assuming that knowledge would help YFull in assigning a more accurate tmrca to our little group of SNP matches. How would I get that information to YFull though, if my second cousin does the Big Y and submits his bam file to YFull?

MitchellSince1893
04-16-2017, 02:23 PM
I have a question. A second cousin who is a 111/111 STR match for me is considering ordering the Big Y. The obvious advantage I can see in his doing that is that we know our exact tmrca: 88 years (using 1950 as the present). That takes us back to our most recent common ancestor, our y-dna great grandfather, who was born 23 October 1862.

I am assuming that knowledge would help YFull in assigning a more accurate tmrca to our little group of SNP matches. How would I get that information to YFull though, if my second cousin does the Big Y and submits his bam file to YFull?

It may be a waste of money. Odds are there will be no SNP difference found by BigY. A more expensive, but more likely to find a SNP difference is testing with FGC. However there is no guarantee it will. On my line two men who share a paternal line ancestor going back to the late 1500s or early 1600s only have 2 novel SNPs for one man (BigY test) and 4 for the other (FGC test). So a 2nd cousin may have no novel SNPs compared to you via a BigY test.

If your goal is to better refine your dating of your branch, you are better off finding a more distant paternal line relative.

I just don't think you are going to advance the cause much with a 2nd cousin BigY test.

Once you get the STR results for you and your relatives from Yfull, use them along with your 111 marker results to get a more refined STR date.

The following is a quote from me in another thread about using up to 400 STRs (more like mid 300s when you combine 111 marker with BigY STR results).

On YFull's STR matching data tool there was 263 STRs compared between Mitchell's FGC test and Guess' FGC test of which 23 were different. Mitchell's BigY test and Guess' FGC test had 259 STRs compared, of which 23 were different (not the exact same 23 markers).

I cut and pasted this YFull data into a spreadsheet, and used the FTDNA 111 marker test results to fill in many blanks in the BigY and FGC test data.

This resulted in ~80 additional STRs (339 markers total) to compare between the two samples, with 29 being different.

I entered this data into the McDonald's TMRCA tool at http://clandonaldusa.org/index.php/tmrca-calculator

...Using 30 years per generation there's a ~50% probability TMRCA lived no later than 1500 AD, and ~97% chance he lived no later than 1300 AD.

As stated earlier, this is more recent than the SNP dating method for TMRCA used by Yfull which is currently ~1000 AD (95% CI 450 AD to 1350 AD).

There is a small overlap between the STR and SNP dating methods (1300 to 1350 AD), so my best guess at the moment is TMRCA for this branch is 1325 AD
http://www.anthrogenica.com/showthread.php?7479-New-branch-under-R-FGC12401-FGC12384&p=213890&viewfull=1#post213890

With the result of another BigY test after I posted the above, I refined this to 1275 AD +/- 75 years. Once Yfull provides STR data for this 3rd kit, I will be able to further refine the estimated date for our paternal line MRCA.

MitchellSince1893
04-16-2017, 02:55 PM
I have a question. A second cousin who is a 111/111 STR match for me is considering ordering the Big Y. The obvious advantage I can see in his doing that is that we know our exact tmrca: 88 years (using 1950 as the present). That takes us back to our most recent common ancestor, our y-dna great grandfather, who was born 23 October 1862.

I am assuming that knowledge would help YFull in assigning a more accurate tmrca to our little group of SNP matches. How would I get that information to YFull though, if my second cousin does the Big Y and submits his bam file to YFull?

Realized I really didn't answer your question. Recommend you ask Vadim on the new Yfull facebook page and ask him directly.

As I indicated above, I don't treat the yfull date as gospel, as I think once you get within the last 1000 years there is this transition between SNP dating and STR dating as to which one is more accurate. SNP dating tends to be older than STR dating. My technique is to use both methods and see if there is an overlap in date ranges.

In this pdf. McDonald gives a good discussion about various dating methods
http://www.jb.man.ac.uk/~mcdonald/genetics/u106-overview-2016.pdf

rms2
04-16-2017, 07:52 PM
Thanks. I was thinking that since I don't know how I and my other Stevens matches are related, perhaps the known tmrca would help out, regardless of the novel SNP picture. It would give YFull a known quantity with which to compare the unknown.

rms2
04-29-2017, 12:35 AM
It's been just over two weeks since one of my same-surname cousins got his Big Y results and asked for the link to his bam file, but he hasn't heard anything from FTDNA.

I emailed them and whined about it, but I have not heard anything back either. Not good.

MitchellSince1893
04-29-2017, 03:06 PM
I don't recall the exact time back in March, but it seems like it took close to 3 weeks to get a bam link.

YFULL just completed the analysis...just waiting for the next version to get the new dates for my branch (FGC12384) based on 4 tests (3 men...one did FGC and BigY).

EDIT: It took 22 days from the time the match results were posted until I got a link (requested as soon as results were available)

rms2
04-29-2017, 07:33 PM
I don't recall the exact time back in March, but it seems like it took close to 3 weeks to get a bam link.

YFULL just completed the analysis...just waiting for the next version to get the new dates for my branch (FGC12384) based on 4 tests (3 men...one did FGC and BigY).

EDIT: It took 22 days from the time the match results were posted until I got a link (requested as soon as results were available)

Thanks. It only took two or three days in my case, so I was starting to worry, plus I am anxious to get the show on the road, which I should have learned by now is not an appropriate attitude in this hobby.

gstockman
04-29-2017, 08:05 PM
Same here.

lgmayka
04-30-2017, 02:32 AM
It's been just over two weeks since one of my same-surname cousins got his Big Y results and asked for the link to his bam file, but he hasn't heard anything from FTDNA.
Has he actually checked to see whether the BAM file is now present? He should not wait for an official email from FTDNA, which may come weeks later.

rms2
04-30-2017, 11:36 AM
Has he actually checked to see whether the BAM file is now present? He should not wait for an official email from FTDNA, which may come weeks later.

I'll ask him. In my emails to him I have just been asking if he got his bam file yet. Honestly, I forgot to tell him to check the "Share BAM" thing for the link. It's been a couple of years since I got mine from FTDNA.

rms2
04-30-2017, 02:22 PM
Has he actually checked to see whether the BAM file is now present? He should not wait for an official email from FTDNA, which may come weeks later.

Thanks, Larry!

You were right, the link was there in the "Share BAM" window in his myFTDNA pages. Wish I had thought to tell him to check there, but, like I said, it's been a couple of years since I got mine. I forgot to tell him how to find it. :doh:

Anyway, he has ordered YFull and sent the link to his bam file to Alex Williamson. Now for more waiting.

rms2
04-30-2017, 07:13 PM
Thanks, Larry!

You were right, the link was there in the "Share BAM" window in his myFTDNA pages. Wish I had thought to tell him to check there, but, like I said, it's been a couple of years since I got mine. I forgot to tell him how to find it. :doh:

Anyway, he has ordered YFull and sent the link to his bam file to Alex Williamson. Now for more waiting.

Actually I had forgotten how the whole thing went two years ago when I got mine. It wasn't until I saw Larry's post that it all came back to me and I thought, "Oh, yeah! That's right: you've got to check that little box!"

Caramba!

rms2
05-07-2017, 12:45 PM
Yesterday over on the YFull Facebook group, Vadim Urasin announced the stats for the forthcoming update of the Tree:



Statistics for the next version 5.04 of our Y-Tree (coming soon):
will be added 2332 SNPs, 303 subclade
by haplogroups:
A00: 1 SNP
A1a: 62 SNPs, 1 subclade
A1b1: 3 SNPs
B: 353 SNPs, 9 subclades
D: 6 SNPs
E: 157 SNPs, 17 subclades
C: 5 SNPs, 1 subclade
G: 88 SNPs, 17 subclades
H: 27 SNPs, 4 subclades
I1: 86 SNPs, 23 subclades
I2: 87 SNPs, 20 subclades
J1: 117 SNPs, 25 subclades
J2: 124 SNPs, 24 subclades
L: 10 SNPs, 3 subclades
T: 166 SNPs, 8 subclades
Q: 156 SNPs, 12 subclades
R1a: 118 SNPs, 19 subclades
R1b: 595 SNPs, 97 subclades
R2: 1 SNP
N: 56 SNPs, 21 subclades
O: 104 SNPs, 2 subclades
others: 10 SNPs
We have used information from samples until YF09368


My 108/111 same-surname match, YF09486, did not make the cut-off, but Vadim assured me he will be in version 5.05.

MitchellSince1893
05-07-2017, 02:44 PM
Looking forward to 5.04. I've got a new kit (YF09234) on my current terminal branch being analyzed at yfull... I'm just awaiting their dating of my branch and of the new sister sub branch that will form.
I've already calculated the new dates using the Yfull formula, but I don't know if yfull will use the same number of combed SNPs that I used. They may find additional ones.

rms2
05-07-2017, 02:52 PM
Looking forward to 5.04. I've got a new kit on my current terminal branch being analyzed at yfull... I'm just awaiting their dating of my branch and of the new sister sub branch that will form.
I've already calculated the new dates using the Yfull formula, but I don't know if yfull will use the same number of combed SNPs that I used. They may find additional ones.

I don't think I will be getting much out of 5.04, but 5.05 should be good for me. If I am really lucky, two more members of my cluster, one of them a 107/111 same-surname match, will get their Big Y results in the meantime and make it into 5.05. At any rate, I've got the 108/111 match I mentioned, YF09486, who should be in version 5.05.

Mikewww
05-08-2017, 01:06 PM
Yesterday over on the YFull Facebook group, Vadim Urasin announced the stats for the forthcoming update of the Tree:

".... R1b: 595 SNPs, 97 subclades ...."

My 108/111 same-surname match, YF09486, did not make the cut-off, but Vadim assured me he will be in version 5.05.

This will be interesting to see how many common SNPs turn up with you and your 108/111 match. I wish had a better idea of the variance and confidence levels we can use with SNP counting based age estimations.

I downloaded the FTDNA and YFull haplotrees for R1b and count the following:

YFull now has a total of 1,372 subclades for R1b
FTDNA now has 3,406.

I expect growth to continue at a rather fast pace. It feels like we had the strongest week ever in terms of Big Y's ordered for the DNA Day sale. On the R1b project, I've seen an increase this year of Big Y results that come in that were not assigned to a subclade of R1b project and sometimes little more than just a surname project. We are picking up in some surname circles. All good.

I think volunteer analysts will not be able to keep up, if they are now. This makes YFull are the more important since they do the real BAM file review and analysis and apparently can do it in a fairly automated method.

MitchellSince1893
05-08-2017, 01:35 PM
...I think volunteer analysts will not be able to keep up, if they are now. This makes YFull are the more important since they do the real BAM file review and analysis and apparently can do it in a fairly automated method.
Alex Williamson's BigTree to do list keeps growing. I'm wondering if he's working on a more automated process.

Mikewww
05-08-2017, 01:54 PM
Alex Williamson's BigTree to do list keeps growing. I'm wondering if he's working on a more automated process.
I have been assuming that but I am not sure any more.

Alex has updated Big Tree to add CombBed region indicators and the so-called "McDonald" regions. U106 is now using the Big Tree technology and it looks like there is a preparation for age estimations, similar to YFull. I thought this all might diminish YFull's attractiveness.

However, it may go the opposite way. Some of these folks work closely with a vendor who probably needs a full "total" haplogroup coverage type tree. ISOGG has not kept up. The Big Tree is focused on VCF files, which is not the right way to go. BAM file analysis is no doubt better even though VCF files can get you about 90 or even 95% of the way home in tree building.

The only thing left standing is YFull, other than FTDNA.

FTDNA's Michael Sager does real BAM file analysis but is request driven. He does not generally have a proactive procedure to add every new Big Y BAM file result added to an experimental tree. So as you might expect, FTDNA has Dr. Behar off doing some kind of work on NGS based tree development.

That's one possible future scenario. It's really Dr. Behar versus YFull in terms of all haplogroup experimental NGS trees although I have my doubts about what Dr. Behar will produce. YFull may try to become "cross-test platform" and add single SNP testing to their tree. I have my doubts about that too as "cross-test platform" comparisons are problematic and can't be highly automated that I can see. Just ask ISOGG or FTDNA's Michael Sager.

rms2
05-08-2017, 02:03 PM
This will be interesting to see how many common SNPs turn up with you and your 108/111 match . . .

We already know he has the usual rack of shared SNPs apparently unique to our line, except that he is FGC36982-. His terminal SNP is listed by FTDNA as FGC36974, which is where I and my 109/111 Stevens match were (and still are on YFull's current tree) until my 108/111 match's Big Y results came in. As a consequence, FTDNA discovered that FGC36982 is downstream of FGC36974 and altered its Haplotree accordingly. Now my 109/111 Stevens match and I are listed by FTDNA as R-FGC36982.

Alex has the three of us on his Big Tree already and shows the same thing.

lgmayka
05-08-2017, 07:10 PM
YFull may try to become "cross-test platform" and add single SNP testing to their tree.
YFull has occasionally accepted single-SNP results for the purpose of disambiguation. But as you say, there may not be any way to automate such inclusion.

One specific example is the E-Z19851 clade (https://yfull.com/tree/E-Z5017/). Its immediate parent Z5017 was a no-call in the BAM files of E-Z19851 men, so by default YFull placed Z19851 as a sibling of Z5017. I sent YFull specific SNP results showing that Z19851+ men were also Z5017+ . YFull then agreed to make Z19851 a subclade of Z5017.

But that required manual effort on everyone's part.

Mikewww
05-08-2017, 07:22 PM
YFull has occasionally accepted single-SNP results for the purpose of disambiguation. But as you say, there may not be any way to automate such inclusion.

One specific example is the E-Z19851 clade (https://yfull.com/tree/E-Z5017/). Its immediate parent Z5017 was a no-call in the BAM files of E-Z19851 men, so by default YFull placed Z19851 as a sibling of Z5017. I sent YFull specific SNP results showing that Z19851+ men were also Z5017+ . YFull then agreed to make Z19851 a subclade of Z5017.

But that required manual effort on everyone's part.

Something to this effect has been posted on a yahoo group forum. He may have misunderstood what was communicated but says one of the vendors says:

... also have a good relationship with ... YFull and there are plans to join forces for developing the tree together since they invest more time to focus on the tree (which is their main business). Our expertise is more at the laboratory technical side.

I can't think of how one can avoid a manual process and some judgement when a full set of phylogenetic equivalents are already on the tree for a branch but a subset from cross-test platforms show new refinements in branching. Maybe this was just an idea under discussion... or maybe the whole idea of combining forces was just related to new WGS test platforms. This actually makes more sense.

rms2
05-08-2017, 10:04 PM
We already know he has the usual rack of shared SNPs apparently unique to our line, except that he is FGC36982-. His terminal SNP is listed by FTDNA as FGC36974, which is where I and my 109/111 Stevens match were (and still are on YFull's current tree) until my 108/111 match's Big Y results came in. As a consequence, FTDNA discovered that FGC36982 is downstream of FGC36974 and altered its Haplotree accordingly. Now my 109/111 Stevens match and I are listed by FTDNA as R-FGC36982.

Alex has the three of us on his Big Tree already and shows the same thing.

Not that anyone cares or should care, but here's what I am talking about from the Big Tree and from FTDNA's Haplotree (with details on the latter added by me):

15744 15745

MitchellSince1893
05-08-2017, 11:47 PM
Not that anyone cares or should care..

It's ok. I have my own current terminal branch thread that's 83% my posts (29 out of 35 posts). Hey when there's 6 known men in the world on this branch and only one is a member of anthrogenica, it's gonna be lonely.

I view these threads as a place to record the history of discovery. One day there will be more members of our respective branches and they may be interested knowing this history.

In the not too distant future some guy is going to get his dna test results from FTDNA, FGC, YSEQ or some future vendor, and he's gonna google his SNP name and your/my thread will pop up and he will make contact with us. That's my hope at least.

Osiris
05-09-2017, 12:26 AM
In the not too distant future some guy is going to get his dna test results from FTDNA, FGC, YSEQ or some future vendor, and he's gonna google his SNP name and your/my thread will pop up and he will make contact with us. That's my hope at least. That's exactly why I went to the the mtDNA forums and created a thread for each one of the lines I'm researching. I put the mutations that weren't on the latest phylotree tree as a cry in the dark for the future people to find me. And the same with the Y lines I'm after.

Mikewww
05-09-2017, 04:56 PM
....
In the not too distant future some guy is going to get his dna test results from FTDNA, FGC, YSEQ or some future vendor, and he's gonna google his SNP name and your/my thread will pop up and he will make contact with us. That's my hope at least.
I think this is an important. Why do we do these things? There are those truly looking for a specific connection, particularly adoptee types of situations. For the majority, I suggest we do this for posterity. We do this for our families in general and our extended families as well as descendants.

If that is the case, on the Y DNA side it is good to get your STRs in to the largest, self-sustaining databases you can and to have your terminal SNP right there too.

It doesn't matter what vendors you do your research with but I think you want to go on record in the largest, self-sustaining genetic genealogy database you can. For the Y DNA, I think that is FTDNA. They've been around, are profitable (some think too much), have the I/T platform, and have the succession plans.

rms2
05-17-2017, 10:58 AM
Looks like the new Tree, version 5.04, is up. Here's the R1b part:

YFull R1b Tree (https://www.yfull.com/tree/R1b/)

rms2
05-19-2017, 12:07 AM
Why is FTDNA's Big Y Matches thing such a mess? Anyone know?

Osiris
05-19-2017, 01:38 AM
It does look bad. I was an early tester of Big Y and when I first tested I had a massive amount of matches and novel variants. And then one day my novel variant count dropped to 2 or 3 for most people I was distantly related to and about 29 for the 2 people I legitimately matched within the last few hundred years. But for my kits that tested 1 year after the debut they never pruned the excess novel variants list. So that makes it difficult to sort through for good matches.

It also looks like they have a list of known SNPs that they use to compare kits and they think you have a match if you have less than 4 SNP differences from that list. Some of my closest matches have 4 SNP differences (F4180 F4346 F2977 YSC0000178) None of those 4 seem like good SNPs to be using for matches. Maybe if they got rid of those from the SNP differences and pruned more faulty novel variants it would look a lot cleaner and be more useful. I should open a contact to try and get them removed.

Mikewww
05-19-2017, 03:37 AM
Why is FTDNA's Big Y Matches thing such a mess? Anyone know?

The person who designed it must not have been a person who understood the volume of Big Y testing and the granularity that would be available in subclades of R1b-L151. They also assumed more consistent coverage from Big Y test run to test run.

The basic flaw is they count total SNPs from the reference model and just assume the most number matching folks are your closest relations.

Who cares about total matching when what you really need is a tree smart matching program that weighs younger SNPs more than older SNPs. The way they do it ends up being who matches you best on Big Y test coverage, not closest relations.

I've told them what I would do to make the matching tree smart and they said they were working on it but anything out of their I/T development is as slow as molasses (as Lawrence would say.):)

Another problem is that when they add SNPs to the haplotree that doesn't get integrated to what the Big Y matching thinks is "known" versus "novel" SNPs. SNPs should flip over in real-time to "known" when added to the haplotree.

Another problem is the Big Y match/results displays are based on the VCF automated calls. These are too rigid and don't filter some regions they should as well as can't dip down and look at low coverage reads (low confidence results) that are good because they are phylogenetically consistent.

A good NGS intepretation should be checking phylogenetic consistency at the same time as region instability problems are assessed.

Still, the Big Y results and matching are useful. Some folks use it to track new Big Y results and contact the new matches and ask them to share their files for analysis.

I've had several cases where I couldn't get the raw files but was still able to get a list of novel and newly discovered as shared SNPs. You have to fool around with the matching tab and look for novel SNPs in common. I've been able to identify new branches and submit them to Michael Sager at FTDNA using this method. He then looks at the BAM files and adds SNPs missing from the Big Y matching/results tab and corrects branching as needed, sometimes even including BAM file results I didn't know about.

Mikewww
05-19-2017, 03:46 AM
Looks like the new Tree, version 5.04, is up. Here's the R1b part:

YFull R1b Tree (https://www.yfull.com/tree/R1b/)

I downloaded the FTDNA haplotree for R1b last night. Here it is in outline format. There are 3,496 branches on the tree.

http://rebrand.ly/R1b-Descendant-Tree-pdf

This is just a different format of what you see when go to your myFTDNA account and click on the haplotree and SNPs button.

As a project administrator I've found the on-line haplotree more useful than I thought. I sign in to the GAP tool and go to "Lab Results Received". I click on each new Big Y (HyNGS) result and each new SNP Pack (SMS) result and go click on that person's haplotree. If you go down to their terminal SNP branch you will see it and the lineage of SNPs above are green. I then click on the "More" button if there are phylogenetic equivalents to see what which ones are green versus red. If you find any red SNPs then you've just broken a phylogenetic block and can report to Sager he needs to add an additional branch point. This is particularly helpful on SNP Packs or new single SNP tests where you don't need to go dig up VCF and BAM files.

RobertCasey
05-19-2017, 03:54 AM
Why is FTDNA's Big Y Matches thing such a mess? Anyone know?

Because everyone blindly gets only Big Y tests vs. a decent percentage of Full Genomes Corp. tests. Also, because everyone is too cheap to pay for good IT support (you want it bundled with a OTC purchase - IT will be minimal with that approach). However, for now, I agree with Mike W on FTDNA for YSTR testing. Even with all the bad things about YSTR reports - it is a viable database. But Big Y gets a grade of D for their level of support. Does anyone seriously use the FTDNA Big Y tools. If you do, you will get very confused and frustrated pretty quickly and will be seeking out FGC and YFULL for more help. Or if you are lucky get free help for R1b from Alex or you are very lucky and have a good admin that analyzes NGS tests.

But the fork in the road is coming very soon. With only a small improvement in read length, we will be able to catch all 111 markers very soon. Also, more are getting interested in 500 STRs as well. If I could just get charting automated in the near future, I would be able to generate mutation rates for all the 500 YSTRs. But we still need to filter out some of the inconsistent types of YSTRs. Also, we can no longer use the FTDNA blended mixture approach of markers at 500 - that would require too large of a sample size (testers) that do not exist at a 20 or 30 % yearly growth rate. Once FGS/WGS provide 111 markers reliably - why would we order a redundant $268 test to enter our data into a database that only supports 111 markers out of 500 ?

Mikewww
05-19-2017, 04:15 AM
Why ?
See what happens when you ask a why question😀

Earl Davis
05-19-2017, 10:34 AM
Why is FTDNA's Big Y Matches thing such a mess? Anyone know?

As well as the issues that Mike just noted the other problem is with relatively modern SNP's that were already known and in the FTDNA database before Big Y was launched. Two of my SNP's were known and in the FTDNA database although they appear to have occurred relatively recently perhaps in the last 800 years or so. Because of this I get to see matches who are related to me within the last 4,000 or so years but do not see some of my more useful close matches because they also have different recent SNP's that were also known before BigY was launched and BigY does not declare a match if there are more than 4 non matching snps that were known back at launch.

Thus I see U152 people in my matches list (I am DF27) but I don't see a guy who I think shares a common ancestor with me around the year 1,200.

rms2
05-19-2017, 10:54 AM
. . .

The basic flaw is they count total SNPs from the reference model and just assume the most number matching folks are your closest relations.
. . .

I figured that was what they were doing, based on what I have seen. I just wondered why, since they should know better, and since they evidently do know better, given that the Haplotree is good and pretty timely.

I definitely agree with Robert that the tools for the Big Y aren't very good. Hopefully some improvements are coming.

Meanwhile, I've got guys in my little haplotype cluster project who are being led by their Big Y Matches page to believe they are closely related to people who aren't even in the same subclade.

rms2
05-19-2017, 11:12 AM
I see that YFull is up to YF09480 on the R1b tree. My 108/111 match is YF09486. Hopefully he'll get a preliminary spot on the tree sometime today.

Mikewww
05-19-2017, 01:38 PM
I definitely agree with Robert that the tools for the Big Y aren't very good. Hopefully some improvements are coming.
I doubt if the Big Y on-line results and matches tab improvements are imminent. It just doesn't feel like a high priority, particularly since Big Y sells like great guns anyway.

However, one should not assume they are sitting still, either on the I/T programmers' keyboards or in the lab. They have real people who do nothing else all day. They have money for capital expenditures. Sooner or later, improvements drip out.

Cofgene
05-19-2017, 04:18 PM
FTDNA seems to have done a good job of removing the "inconsistent" BigY calls from results posted in 2017. They haven't cleaned up the historical calls and still spit out ancestral = derived calls where individuals don't share any singletons.

I think all of us should be pushing FTDNA to provide an updated analysis of existing BigY results against the current human reference genome. With that transition they can also a) clean up how they are reporting known and novels, and b) provide STR calls via something like lobSTR. Now maybe for existing BigY's they could try to get $19.99 for access to the new realigned results STR calls......

A second item is that we should be strongly encouraging FTDNA to offer a higher resolution wgs based test as BigY v2 and get off of doing the stupid data scrubbing efforts which hurt current BigY results. With FTDNA offering a higher resolution test we will have a better chance of addressing y-haplotree structural problems that BigY results have introduced.

rms2
05-19-2017, 11:19 PM
I see that YFull is up to YF09480 on the R1b tree. My 108/111 match is YF09486. Hopefully he'll get a preliminary spot on the tree sometime today.

Well, YFull's R1b tree has not budged beyond ID #YF09480, so I guess I was wrong. Aarrgghh!

lgmayka
05-20-2017, 01:19 AM
Well, YFull's R1b tree has not budged beyond ID #YF09480, so I guess I was wrong. Aarrgghh!
Maybe Russia has been asleep. They're in a different time zone, you know. :)

dp
05-20-2017, 03:57 PM
It's ok. I have my own current terminal branch thread that's 83% my posts (29 out of 35 posts). Hey when there's 6 known men in the world on this branch and only one is a member of anthrogenica, it's gonna be lonely.

I view these threads as a place to record the history of discovery. One day there will be more members of our respective branches and they may be interested knowing this history.

In the not too distant future some guy is going to get his dna test results from FTDNA, FGC, YSEQ or some future vendor, and he's gonna google his SNP name and your/my thread will pop up and he will make contact with us. That's my hope at least.
did the same thing. Best I can tell there are less than a dozen on the I-S18218 branch. Check out: this thread
dp :-)

lgmayka
05-20-2017, 09:21 PM
My 108/111 match is YF09486. Hopefully he'll get a preliminary spot on the tree sometime today.
He's there (https://yfull.com/tree/R-FGC36974/) now. YFull is up to at least YF09529 (https://yfull.com/tree/R-FGC57007/).

rms2
05-21-2017, 04:03 PM
He's there (https://yfull.com/tree/R-FGC36974/) now. YFull is up to at least YF09529 (https://yfull.com/tree/R-FGC57007/).

Thanks. I was in New York City all day yesterday, with my wife dragging me hither and yon, so I did not see that until this morning.

The next version of the tree (5.05) should see FGC36982 moved downstream of FGC36974, and IDs YF08619 (my 109/111 match) and YF08577 (me) moved to FGC36982.

We've got another guy with our surname, a 107/111 match for me, awaiting his Big Y results. Hope they come in time for version 5.05.

rms2
05-22-2017, 01:43 AM
My STRs came in this evening. I did not count how many there are, but there are a few not showing, so something just under 500, I guess.

rms2
05-23-2017, 11:23 PM
YFull's site has been down the last couple of days. Over on the Facebook group, Roman Sychev says it's for maintenance and sorry for the inconvenience. Okay. Hope it's back up soon.

I remember Roman from quite a few years back over on FTDNA's forum, before he got his first y-dna test results.

lgmayka
05-24-2017, 01:26 PM
Over on the Facebook group, Roman Sychev says it's for maintenance and sorry for the inconvenience.
Frankly, "unscheduled maintenance" is often a euphemism for a malware attack (which may require upgrading the operating system, installing a better protection system, etc.). But that's just my personal suspicion.

rms2
05-25-2017, 11:06 AM
Frankly, "unscheduled maintenance" is often a euphemism for a malware attack (which may require upgrading the operating system, installing a better protection system, etc.). But that's just my personal suspicion.

I hope YFull wasn't too badly damaged or compromised. It seems to be taking them awhile to come back online.

MacUalraig
05-25-2017, 11:23 AM
It's only now I've come to see how dependent I am on their tree so want to see it back up asap.

Dubhthach
05-25-2017, 11:53 AM
Frankly, "unscheduled maintenance" is often a euphemism for a malware attack (which may require upgrading the operating system, installing a better protection system, etc.). But that's just my personal suspicion.

Working in IT operations as I do, I think ye might be onto something there.

JMcB
05-25-2017, 02:38 PM
Quote Originally Posted by lgmayka:
Frankly, "unscheduled maintenance" is often a euphemism for a malware attack (which may require upgrading the operating system, installing a better protection system, etc.). But that's just my personal suspicion.


Working in IT operations as I do, I think ye might be onto something there.

They did say on their Facebook page that they were the victims of a "bot"(?) attack, where they were bombarded with thousands of simultaneous requests to view their tree. However, they did say later - in response to the concerns of their customers - that their subsequent maintenance was not related to that attack. I report, you decide ;-)

Dubhthach
05-25-2017, 03:42 PM
There's a reason why Cloudflare makes a profit when it comes to mitigating DDoS etc. :)

Still a maintenance window shouldn't really be longer than 2-3 hours, if you are down for more than a day -- well you have serious issues. Could be simply case of hardware outage taking down their backend system (lack of backups will kill you there! :) )

Mikewww
05-25-2017, 05:56 PM
Frankly, "unscheduled maintenance" is often a euphemism for a malware attack (which may require upgrading the operating system, installing a better protection system, etc.). But that's just my personal suspicion.
I am suspicious based on a conversation I had with a genetic genealogist blogger who has had dealing with them in the past when there was a problem. These are not necessarily simple or random problems.

I'm happy with what YFull has provided me and would like to see more L513 people use it so they improve their TMRCA dating.

However, the cyber world is not all nice and there is so much that goes on that we know almost nothing about. I'm just speculating, but I am suspicious. The alternative thinking would relate to operational incompetence but I don't think that is so.

Dubhthach
05-26-2017, 08:35 AM
Well they seem to be back up and running this morning.

thewarrider7
05-28-2017, 03:28 PM
Hi Dubhthach,

Ive read many of your post and i got my results back today.

I am english and my last name is Snooks.

However, R-P312/S116 > Z290 > L21/S145 > DF13 > FGC5494 > FGC5561 > FGC7448 > FGC5496 > FGC5521 > FGC5549 > FGC5511 > FGC5517 > 7564743-C-A
is atlantic celtic?

Snooks is found in hampshire where the belgic celtic tribes settled?

Although my big y test closest matches are north of england borderlands/ Scottish south west and isle of manx

Any ideas?

Kind regards

rms2
05-28-2017, 03:38 PM
Hi Dubhthach,

Ive read many of your post and i got my results back today.

I am english and my last name is Snooks.

However, R-P312/S116 > Z290 > L21/S145 > DF13 > FGC5494 > FGC5561 > FGC7448 > FGC5496 > FGC5521 > FGC5549 > FGC5511 > FGC5517 > 7564743-C-A
is atlantic celtic?

Snooks is found in hampshire where the belgic celtic tribes settled?

Although my big y test closest matches are north of england borderlands/ Scottish south west and isle of manx

Any ideas?

Kind regards

I know you addressed your post to Paul, but I can't resist giving some advice that has really benefited me and quite a few others.

You should send your VCF file and your STR markers to Alex Williamson for analysis and inclusion in his Big Tree. It's free (which is amazing, considering the work Alex does). Here's how:

Instructions (http://www.ytree.net/Instructions.html)

Here is the section of Alex's Big Tree for FGC5494 (your subclade under DF13): FGC5494 (http://www.ytree.net/DisplayTree.php?blockID=18)

You should also send your BAM file to YFull for their analysis. Their service costs $49, but it's worth much more than that.

thewarrider7
05-28-2017, 04:07 PM
Hi rich,

Yes i am shooting out to all the experts hopefully i will get some useful info on the genetic heritage.

I have done that already and i have been placed with Jackson. I come under Snooks.

I was told to do the Big y for this reason but it has revealed very little information to me.

Jackson believes his heritage is from england and the name is from the borderlands but thats all i have got for 300 odd quid lol.

rms2
05-28-2017, 05:58 PM
Hi rich,

Yes i am shooting out to all the experts hopefully i will get some useful info on the genetic heritage.

I have done that already and i have been placed with Jackson. I come under Snooks.

I was told to do the Big y for this reason but it has revealed very little information to me.

Jackson believes his heritage is from england and the name is from the borderlands but thats all i have got for 300 odd quid lol.

Well, dna testing takes time to produce results. I got my first 37-marker test from FTDNA back in the spring of 2006, and it has taken all that time to really reap the full benefits. Along the way I have learned a lot and found it all very entertaining and enlightening. I have never regretted any of the money I have spent on genetic genealogy.

rms2
05-29-2017, 02:33 PM
Here's something curious. My STRs came in a couple of days ago at YFull, and apparently I got 443 out of the 500 possible (88.6%). I have one close match thus far, a man with my surname who matches me 109/111 at FTDNA. At YFull he matches me 284/285. Apparently he only got 286 STRs out of the possible 500 (57.2%). That seems rather low. What gives?

This man also shares my terminal SNP, FGC36982, and likely the same 4th or 5th y-dna great grandfather.

MitchellSince1893
05-29-2017, 03:04 PM
Here's something curious. My STRs came in a couple of days ago at YFull, and apparently I got 443 out of the 500 possible (88.6%). I have one close match thus far, a man with my surname who matches me 109/111 at FTDNA. At YFull he matches me 284/285. Apparently he only got 286 STRs out of the possible 500 (57.2%). That seems rather low. What gives?

This man also shares my terminal SNP, FGC36982, and likely the same 4th or 5th y-dna great grandfather.
You are fortunate to have so many, The 3 samples I have at Yfull have 422 STRs for my father's BigY, 321 STRs for his FGC kit, and 303 STRs for another FGC kit. Which results in 259 to 268 STRs to compare among the 3 kits..

What you can do is create a spreadsheet, and fill in some of the holes by combining the 111 marker with BigY results. I was able to get an additional ~80 STRs to compare.

http://www.anthrogenica.com/showthread.php?7479-New-branch-under-R-FGC12401-FGC12384&p=213890&viewfull=1#post213890

rms2
05-29-2017, 05:37 PM
It's too bad FTDNA has let Ysearch pretty much fall to rack and ruin. It would be great if it had the capability of handling 500 STR markers and making comparisons based on them.

rms2
05-29-2017, 05:58 PM
. . .

What you can do is create a spreadsheet, and fill in some of the holes by combining the 111 marker with BigY results. I was able to get an additional ~80 STRs to compare . . .

That sounds like a lot of work for little return, unless there is an easy way to copy and paste.

Update: I caught the little "download csv" button finally and did that. I just need to go back and fill in the gaps where I can.

thewarrider7
05-29-2017, 07:28 PM
Well, dna testing takes time to produce results. I got my first 37-marker test from FTDNA back in the spring of 2006, and it has taken all that time to really reap the full benefits. Along the way I have learned a lot and found it all very entertaining and enlightening. I have never regretted any of the money I have spent on genetic genealogy.

Aye i dont regret it as i find it very fascinating and have branched deeper into my knowledge of history and genetics.

I am just slightly disappointed with the big y as it didnt tell me a lot really.

rms2
05-29-2017, 08:12 PM
Aye i dont regret it as i find it very fascinating and have branched deeper into my knowledge of history and genetics.

I am just slightly disappointed with the big y as it didnt tell me a lot really.

Well, I did the Big Y back in 2015 and it only recently started to produce real benefits, as more of my STR matches started to test. I proactively recruited them and bugged them to test, however. I did not just sit back and wait.

My closest same-surname match (other than a known second cousin, who matches me exactly), 109/111, began back in the summer of 2016 as someone I contacted at Ancestry.com because I thought he might be a relative. I did not know him from Adam and he did not know me. He was a little reticent at first, but once he got his 111-marker results and saw our match, he realized I wasn't kidding and wasn't trying to con him out of money. He caught fire and has been a real stalwart ever since. I did not have to talk him into the Big Y or YFull. He did those things on his own.

rms2
06-16-2017, 02:17 PM
We should be getting close to time for the new YFull tree, version 5.05. Version 5.04 was posted a month ago tomorrow. (http://www.anthrogenica.com/showthread.php?9633-Big-Y-What-Now&p=235667&viewfull=1#post235667)

rms2
06-16-2017, 02:31 PM
We should be getting close to time for the new YFull tree, version 5.05. Version 5.04 was posted a month ago tomorrow. (http://www.anthrogenica.com/showthread.php?9633-Big-Y-What-Now&p=235667&viewfull=1#post235667)

The update before that, version 5.03, was posted 09 April. (http://www.anthrogenica.com/showthread.php?9633-Big-Y-What-Now&p=225649&viewfull=1#post225649)

JMcB
06-16-2017, 03:47 PM
We should be getting close to time for the new YFull tree, version 5.05. Version 5.04 was posted a month ago tomorrow. (http://www.anthrogenica.com/showthread.php?9633-Big-Y-What-Now&p=235667&viewfull=1#post235667)

If I remember correctly, they may be running a little late this month because they have a lot of results from scientific papers to process.

NiloSaharan
06-16-2017, 04:29 PM
If I remember correctly, they may be running a little late this month because they have a lot of results from scientific papers to process.

I think that's correct, Vadim Urasin mentioned this on Yfull's fb group (https://www.facebook.com/groups/yfull/) on June 9th:


"We have registered ID YF10000 yesterday. A milestone. Thank you all for orders. By the way, in this batch we have added about a hundred samples from scientific papers of this year (later I will write references to papers). They have a lot of new SNPs. This is a main reason of delay with results"

-also eagerly anticipating some results

lgmayka
07-02-2017, 12:16 PM
We should be getting close to time for the new YFull tree, version 5.05. Version 5.04 was posted a month ago tomorrow. (http://www.anthrogenica.com/showthread.php?9633-Big-Y-What-Now&p=235667&viewfull=1#post235667)
As far as I can tell, YFull has completed analysis of all posted entries--the most recent is YF10009 (https://yfull.com/tree/R-Y16854*/). YFull now has to make all necessary adjustments in the haplotree to accommodate the many hundreds of new entries. My own guess is that we will see 5.05 in a week or two.

rms2
07-02-2017, 12:24 PM
As far as I can tell, YFull has completed analysis of all posted entries--the most recent is YF10009 (https://yfull.com/tree/R-Y16854*/). YFull now has to make all necessary adjustments in the haplotree to accommodate the many hundreds of new entries. My own guess is that we will see 5.05 in a week or two.

I hope so. This new iteration will be significant for my own personal genetic genealogy. Unfortunately a couple of new entries from our little group did not make it in in time and will have to wait for the edition after this coming one.

When you get into this hobby, someone ought to play you that Tom Petty song, The Waiting, just to give you an idea of what you're in for.


https://www.youtube.com/watch?v=uMyCa35_mOg

Volat
07-02-2017, 01:10 PM
A person I know is interested in genetic genealogy. He had Y-DNA 67 marker done at FTDNA. He was considering Big Y and YSEQ. He chose YSEQ for financial reasons. YSEQ determined his terminal SNP at yfull tree. He paid $88 to YSEQ.

rms2
07-02-2017, 08:55 PM
Roman Sychev just posted over on the YFull Facebook group that the new tree should be out 15-20 July.

Seems like a long time to wait.

rms2
07-02-2017, 10:24 PM
I have three more members of my little haplotype cluster who won't make version 5.05 but should make the one after it, 5.06: two obvious relatives with the surnames Stevens and Stephens, and another slightly more distant match with the surname Webb.

Wish they had all managed to make it to YFull in time for this coming update, but you all know how this stuff goes (see the Tom Petty song in post #170 above).

JohnHowellsTyrfro
07-03-2017, 07:05 AM
I've been putting off doing Big Y for years mainly because of cost but partly because I didn't think it would tell me very much.
I eventually did a 67 marker test and surprisingly that showed a paternal line connection with the Cecils ( William Cecil 1st Baron Burghley etc.). I was aware before that Cecil descendants were also U106 Z326 and that my own and Cecil ancestry was apparently in West Herefordshire/Wales border but I thought that likely to be coincidence.
Following the 67 marker results I had to do Big Y and am expecting results in a few weeks although I still don't know if it will tell me very much more other than maybe helping to narrow down when the common ancestor was. I've been trying to do a crash course on Cecil ancestry. There are unreliable historic claims about the Cecils having Welsh origins, in fact I think until fairly recently it was even doubted that they had a family connection to West Herefordshire.
"Their family’s humble origin was to be often used to denigrate William and Robert Cecil. Its fortunes were founded by David Cecil’s service with Sir David Philip, who may have been his uncle. After perhaps fighting alongside him at Bosworth, " (The History of Parliament).
If my shared ancestry is a long time ago maybe pre-conquest it would seem to put that (Cecil line) ancestry in or near Wales early on. That would still leave the question for me of whether they might have had Anglo Saxon origins or indeed have been U106 and Welsh? There seems little doubt that "Seisil" is a name of Welsh origin, as is my own surname but that may not prove anything.
Any thoughts on what I should be looking for in my Big Y results would be appreciated. John

MacUalraig
07-03-2017, 07:57 AM
Any thoughts on what I should be looking for in my Big Y results would be appreciated. John

First thing to do is request your BAM file via the helpdesk (its the first topic option in the list on the contact form) and submit it to www.YFull.com. They will give you an advanced GUI to access your raw data, view novel variants, extract hundreds of STRs and do both SNP and STR matching AND put you on their Y tree. You may pick up matches from other sequencing firms too. One of the big pluses for them is that their matching is a lot easier to figure out than what familytree offer which can be confusing at times.

JohnHowellsTyrfro
07-03-2017, 08:36 AM
First thing to do is request your BAM file via the helpdesk (its the first topic option in the list on the contact form) and submit it to www.YFull.com. They will give you an advanced GUI to access your raw data, view novel variants, extract hundreds of STRs and do both SNP and STR matching AND put you on their Y tree. You may pick up matches from other sequencing firms too. One of the big pluses for them is that their matching is a lot easier to figure out than what familytree offer which can be confusing at times.

Thank you for that. I will do my best, although my understanding of the technicalities is limited. :) John

rms2
07-03-2017, 12:45 PM
I don't know how reliable this is, but I read that the Cecil family came from Flanders originally, possibly with the contingent of Flemings who were part of William the Conqueror's army. Have you heard that?

ArmandoR1b
07-03-2017, 01:20 PM
I've been putting off doing Big Y for years mainly because of cost but partly because I didn't think it would tell me very much.
I eventually did a 67 marker test and surprisingly that showed a paternal line connection with the Cecils ( William Cecil 1st Baron Burghley etc.). I was aware before that Cecil descendants were also U106 Z326 and that my own and Cecil ancestry was apparently in West Herefordshire/Wales border but I thought that likely to be coincidence.
Following the 67 marker results I had to do Big Y and am expecting results in a few weeks although I still don't know if it will tell me very much more other than maybe helping to narrow down when the common ancestor was.

Any thoughts on what I should be looking for in my Big Y results would be appreciated. John

Out of curiosity, how many matches do you have at Y67 and what is the GD with them? How many of them have had a BigY test? Is Z326 the youngest SNP that they show to have?

JohnHowellsTyrfro
07-03-2017, 06:23 PM
I don't know how reliable this is, but I read that the Cecil family came from Flanders originally, possibly with the contingent of Flemings who were part of William the Conqueror's army. Have you heard that?

No I haven't read that but I have wondered about the possibility of a Norman connection. This link from the National Library of Wales refers to the apparent origins of the family in West Herefordshire, starting with Robert Sitsyllt, a follower of Robert Fitzhamon (Robert of Gloucester).
https://www.google.co.uk/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=0ahUKEwjRv5vs2O3UAhWhCcAKHeFqCoQQFggvMAE&url=http%3A%2F%2Fyba.llgc.org.uk%2Fen%2Fs-CECI-ALL-1450.html&usg=AFQjCNHVHUvMB9YzbEVsY4_RR6QPacVbrA

Before this it all seems quite murky. Burghley himself had a pedigree drawn up which showed noble Welsh descent but I think that is regarded as pretty dubious.
There are various theories on the possible family origins. There is one claim that it is Romano British from the name Cecilius (not sure If I spelt that correctly) some say it is connected with Sicily. Jean Manco kindly pointed out that in the Domesday Book a Saissil or Sassil held land at Lyde and Staunton on Arrow ( West Herefordshire) prior to the Conquest with speculation in Pase Domesday that he could have been a Welsh ally of Harold Godwinson. Of course could just be coincidence.
I have recently contacted Hereford Records Office researchers asking if they can find any connection. One of my 19th Century ancestors was farming "Old Hay" which I've recently found out is very near or part of Urishay castle the seat of the De La Hay family which were connected to the Cecils through marriage. Aware of course that a NPE somewhere down the generations is a possibility but I don't think it is before the mid- 1700's (if at all) owing to autosomal matches with other Howells family descendants from that period.
John

JohnHowellsTyrfro
07-03-2017, 06:44 PM
Out of curiosity, how many matches do you have at Y67 and what is the GD with them? How many of them have had a BigY test? Is Z326 the youngest SNP that they show to have?

Please excuse my limited technical knowledge in replying. There are a number of families which appear to share paternal descent with the Cecils. The 67 marker results appear to show a close relationship with one family branch but to be honest I'm a bit dubious about the closeness of the relationship based only on the FTDNA comparison method which I understand has it's limitations in terms of accuracy ( failure to consider no-calls, possible convergence etc). Others have also also recently taken the Big Y test and our results are expected about the same time.
When I have my results I prefer to place it in the hands of the U106 project group who I think will be more rigorous and accurate in their analysis. I'm told the current estimate for the SNP (FGC3946) that we all share is 910AD but at least one branch seems to have split off sometime before 1388 from what I have been told.
Hopefully the Big Y results may bring a bit more information. John

JohnHowellsTyrfro
07-03-2017, 06:58 PM
I don't know how reliable this is, but I read that the Cecil family came from Flanders originally, possibly with the contingent of Flemings who were part of William the Conqueror's army. Have you heard that?

One small thing I didn't mention is that I have an exact 12 marker match with a chap who has farming ancestry near Brecon back to the 1700's (my only "exact" match in the UK). I must admit I have been tempted to consider that there could indeed be a paternal line connection between the Cecils and Vaughans of Tretower who themselves I believe claim descent from Walter Sais. Perhaps 12 markers is too uncertain? John

https://www.google.co.uk/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=0ahUKEwjL4_3w5O3UAhUGKcAKHXWCBMIQFgg0MAI&url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FRoger_ Vaughan_of_Bredwardine&usg=AFQjCNGWBVTR_raQoarkmr8whXLFNKU39g

ArmandoR1b
07-03-2017, 07:27 PM
Please excuse my limited technical knowledge in replying. There are a number of families which appear to share paternal descent with the Cecils. The 67 marker results appear to show a close relationship with one family branch but to be honest I'm a bit dubious about the closeness of the relationship based only on the FTDNA comparison method which I understand has it's limitations in terms of accuracy ( failure to consider no-calls, possible convergence etc). Others have also also recently taken the Big Y test and our results are expected about the same time.
When I have my results I prefer to place it in the hands of the U106 project group who I think will be more rigorous and accurate in their analysis. I'm told the current estimate for the SNP (FGC3946) that we all share is 910AD but at least one branch seems to have split off sometime before 1388 from what I have been told.
Hopefully the Big Y results may bring a bit more information. John

It's because of problems such as convergence that Next Generation Sequencing is needed to determine genetic branching of ancestors in the direct paternal line but the GD provided can still be used as a rough guide which is why I was curious as to what you have especially since it goes back to 910 AD. It's interesting that YFull shows FGC3946 (https://www.yfull.com/tree/R-Y20959/) to have a TMRCA of between 1100 and 375 years before present. The older date is in agreement with the current estimate of 910 AD that you were given. I would think that you have some matches with a GD of 4 or more.

JohnHowellsTyrfro
07-03-2017, 08:32 PM
It's because of problems such as convergence that Next Generation Sequencing is needed to determine genetic branching of ancestors in the direct paternal line but the GD provided can still be used as a rough guide which is why I was curious as to what you have especially since it goes back to 910 AD. It's interesting that YFull shows FGC3946 (https://www.yfull.com/tree/R-Y20959/) to have a TMRCA of between 1100 and 375 years before present. The older date is in agreement with the current estimate of 910 AD that you were given. I would think that you have some matches with a GD of 4 or more.

Thank you. The thing is, these estimates are quite broad. I guess that if around 900 AD is reasonably accurate that might suggest that the common ancestor was in Britain before the conquest, unless it is possible to identify matches on the continent?
When I get my results I will try and find out what I can.
Mr. Robert Casey commented on the U106 project group. I can't pretend to fully understand his comment, but it seems to me things can't always be taken at face value.
"For much younger haplogroups, (1,500 to 2,500 years old), you can have another form of convergence where there is really a "lack of divergence" during the last couple of thousand of years. For R-L226, we have a very unique YSTR signature at 67 markers (pretty common). We estimate the age when R-L226 became prolific is around 1,500 years ago (but the real age of R-L226 is much older due dozens of L226 equivalents found - again not that uncommon for R-L21 haplogroups). During the last 1,500 years, we have around ten percent of members of the L226 that have between a 80 to 90 % false hit rate at 67 markers. We now know these are false positives since we now have 50 known YSNP branches under L226 now." John

ArmandoR1b
07-04-2017, 12:42 PM
Thank you. The thing is, these estimates are quite broad. I guess that if around 900 AD is reasonably accurate that might suggest that the common ancestor was in Britain before the conquest, unless it is possible to identify matches on the continent?
When I get my results I will try and find out what I can.
Mr. Robert Casey commented on the U106 project group. I can't pretend to fully understand his comment, but it seems to me things can't always be taken at face value.
"For much younger haplogroups, (1,500 to 2,500 years old), you can have another form of convergence where there is really a "lack of divergence" during the last couple of thousand of years. For R-L226, we have a very unique YSTR signature at 67 markers (pretty common). We estimate the age when R-L226 became prolific is around 1,500 years ago (but the real age of R-L226 is much older due dozens of L226 equivalents found - again not that uncommon for R-L21 haplogroups). During the last 1,500 years, we have around ten percent of members of the L226 that have between a 80 to 90 % false hit rate at 67 markers. We now know these are false positives since we now have 50 known YSNP branches under L226 now." John

A lot of people have argued against using NGS testing because they think that using STRs is good enough. The situation that you have pointed out is a very good example of why NGS is better and the possibility of that was why I had the questions. Having the range of GD of the matches at 67 markers would help point out even more of how good of an example it is. Basically, there becomes a point where STRs aren't very useful for branching and what I am looking for is more evidence beyond the kits that I have seen.

rms2
07-04-2017, 01:27 PM
It seems to me STRs are good at getting people into genetic genealogy because they are relatively inexpensive compared with NGS testing. They can be used for branching if one has sufficient matches, but they certainly are less precise than NGS SNP testing. In both cases, STR and SNP testing, one needs some close matches to get the full benefit of the testing.

STR testing has been good to me, but NGS testing has really fleshed out and brought into focus the somewhat hazier picture first captured by STRs.

rms2
07-08-2017, 02:27 PM
Vladimir Semargl posted the following on the YFull Facebook page this morning:



Statistics for the next version 5.05 of our Y-Tree (coming soon):
will be added 3171 SNPs, 602 subclades
by haplogroups:
A1a: 1 SNP
A1b1: 4 SNPs, 3 subclades
B: 577 SNPs, 45 subclades
D: 368 SNPs, 4 subclades
E: 91 SNPs, 21 subclades
C: 41 SNPs, 3 subclades
G: 37 SNPs, 10 subclades
H: 125 SNPs, 16 subclades
I1: 199 SNPs, 60 subclades
I2: 121 SNPs, 44 subclades
J1: 129 SNPs, 33 subclades
J2: 365 SNPs, 39 subclades
L: 78 SNPs, 19 subclades
T: 17 SNPs, 13 subclades
Q: 86 SNPs, 14 subclades
R1a: 207 SNPs, 68 subclades
R1b: 510 SNPs, 170 subclades
R2: 40 SNPs, 8 subclades
N: 64 SNPs, 19 subclades
O: 85 SNPs, 9 subclades
others: 26 SNPs
others: 4 subclades
We have used information from samples until YF010010

Dave-V
07-08-2017, 05:06 PM
It seems to me STRs are good at getting people into genetic genealogy because they are relatively inexpensive compared with NGS testing. They can be used for branching if one has sufficient matches, but they certainly are less precise than NGS SNP testing. In both cases, STR and SNP testing, one needs some close matches to get the full benefit of the testing.

STR testing has been good to me, but NGS testing has really fleshed out and brought into focus the somewhat hazier picture first captured by STRs.

Agreed. Say what you will about FTDNA's product practices (please don't :)) about requiring STRs before NGS testing, but the end result is STRs are pretty pervasive among tested members. Whereas SNP testing is more precise but has less broad coverage, certainly when it comes to NGS testing. IMHO we'll still be in the situation of needing both for the immediate future.

I agree with Robert Casey that STRs are really only useful within about a 2000 (I'd go to 2500) ybp timeframe. At that limit you already have to start ignoring many of the more frequently-mutating markers because they get too noisy for any useful analysis. But within that timeframe it's not just STR genetic distance that's important, it's also "signatures" - patterns of off-modals that are shared by people with common lines of descent. At 67-111 markers you've got a lot of possible signatures to show branching. Most groups don't have the SNP coverage (yet) to delineate ALL their branches so STR testing is important.

Once everyone is routinely NGS-tested people say "we won't need STRs" but we may really still need them for branches where SNPs have mutated much more slowly than average or where people really don't have ANY genealogy information even as to their father or grandfather etc since SNPs occur every 3-4 generations. But extensive SNP testing will also mean we'll have more accurate data on STR mutation rates, convergence, and ancestral haplotypes so extensive SNP coverage may actually improve STR-based analysis too. Not to mention the explosion of available STRs if NGS testing continues to report 500+ STRs as well.

In the meantime, SNP-based TMRCAs or SNP age estimates are only possible using NGS testing so their coverage and accuracy is only as good as the percentage of NGS tests within a group. STR-based age estimates can fill in the blanks. Neither is (to my knowledge) necessarily better or worse than the other; they are just both significantly affected by the fluctuations in mutation rates (STR or SNP) within a subgroup as compared to statistical "norms" which means either can have a smaller or larger error margin within any given small sample size.

rms2
07-19-2017, 01:40 PM
Vladimir Semargl posted the following on the YFull Facebook page this morning:



Statistics for the next version 5.05 of our Y-Tree (coming soon):
will be added 3171 SNPs, 602 subclades
by haplogroups:
A1a: 1 SNP
A1b1: 4 SNPs, 3 subclades
B: 577 SNPs, 45 subclades
D: 368 SNPs, 4 subclades
E: 91 SNPs, 21 subclades
C: 41 SNPs, 3 subclades
G: 37 SNPs, 10 subclades
H: 125 SNPs, 16 subclades
I1: 199 SNPs, 60 subclades
I2: 121 SNPs, 44 subclades
J1: 129 SNPs, 33 subclades
J2: 365 SNPs, 39 subclades
L: 78 SNPs, 19 subclades
T: 17 SNPs, 13 subclades
Q: 86 SNPs, 14 subclades
R1a: 207 SNPs, 68 subclades
R1b: 510 SNPs, 170 subclades
R2: 40 SNPs, 8 subclades
N: 64 SNPs, 19 subclades
O: 85 SNPs, 9 subclades
others: 26 SNPs
others: 4 subclades
We have used information from samples until YF010010


"Coming soon" must mean something different to Vladimir than it does to me.

Still waiting.

Joe B
07-19-2017, 03:31 PM
Quite a few of the STR results were released in the last day or two. Let's hope that's a precursor to a haplotree update.

rms2
07-22-2017, 04:49 PM
Dang! Still waiting.

Monday maybe?

rms2
07-30-2017, 01:20 PM
YFull's new tree, version 5.05, is finally up. Here is the R1b part:

R1b Tree (https://www.yfull.com/tree/R1b/)

rms2
09-28-2017, 12:17 AM
YFull's latest y-dna tree, version 5.06, is available.

The R1b Tree (https://www.yfull.com/tree/R1b/) brought some big news for my y-dna relatives, breaking out another line below FGC36974: PF5064. This should help the two guys on that line better direct their genealogical efforts.

rms2
11-05-2017, 07:41 PM
YFull's latest y-dna tree, version 5.07, is available.

Here (https://www.yfull.com/tree/R1b/) is the R1b part.

No changes for my group, but we're still waiting for three new Big Ys, thanks to Hurricane Harvey and HG38.

rms2
11-05-2017, 09:16 PM
YFull's latest y-dna tree, version 5.07, is available.

Here (https://www.yfull.com/tree/R1b/) is the R1b part.

No changes for my group, but we're still waiting for three new Big Ys, thanks to Hurricane Harvey and HG38.

Anybody get anything big out of version 5.07?

sgdavies@hotmail.com
11-29-2017, 09:43 AM
Just got my Big Y result, no idea what it means, no matches anywhere, also I wanted to request the BAM file, but when I click on url link to form and fill out info, then submit, nothing happens.. :argue:

Wing Genealogist
11-29-2017, 11:38 AM
FTDNA has stated they will be notifying everyone when they are ready to process BAM file requests. They still have not finished the Build 38 conversion process. I checked the U106 Project and we apparently have at least 29 individuals (some who ordered the test early in 2014) who are listed as still pending their (new) results.

Given FTDNA's less than stellar track record with IT issues, it wouldn't surprise me if this number is not correct (and it could be more or less individuals).

rms2
11-29-2017, 12:01 PM
In the meantime, YFull quietly snuck in its new version of the tree, 5.08. That was quick!

Here (https://yfull.com/tree/R1b/) is the R1b section.

One of the Big Y's I was waiting for came in late last night or early this morning, but since BAM files aren't available, we'll have to wait on getting YFull's service.

rms2
11-29-2017, 12:34 PM
I just noticed the nice little national flags next to the YFull ID numbers now. Looking good! They make spotting the ancestral origin of the entries much easier than before.

Mikewww
11-29-2017, 05:53 PM
Just got my Big Y result, no idea what it means, no matches anywhere, also I wanted to request the BAM file, but when I click on url link to form and fill out info, then submit, nothing happens.. :argue:

As has been mentioned, we'll have to wait before getting your BAM files.

However, usually the Big Y Raw Results VCF/BED files are available almost immediately. Those are used or a free analysis and interpretation in the Big Tree and TMRCA Age estimates. We can thank two super analysts, Alex Williamson and Iain McDonald for supporting these analyses and James Kane for setting up a data warehouse.

If you get your information uploaded to the James Kane warehouse you will automatically be added to the Williamson and McDonald analyses.

http://haplogroup-r.org/submit_data.php

This works for everyone in R1b-L151, which is mostly P312 and U106. This includes large sublades like L21, M222, U152, DF27 and DF19.


The Big Tree:

http://ytree.net/
http://www.ytree.net/DisplayTree.php?blockID=1147

Age estimates:

http://www.jb.man.ac.uk/~mcdonald/genetics/p312/table.html
http://www.jb.man.ac.uk/~mcdonald/genetics/table.html

This does not mean you shouldn't do paid for services like YFull but these are free so I'd jump on them.

sgdavies@hotmail.com
11-29-2017, 06:30 PM
Thanks Mike!

Osiris
11-29-2017, 06:56 PM
Just got my Big Y result, no idea what it means, no matches anywhere, also I wanted to request the BAM file, but when I click on url link to form and fill out info, then submit, nothing happens.. :argue:
Did you check the box that asks if you're a robot? I opened the page in Chrome and that robot thing wasn't there. Since I didn't see it, didn't know it was there and couldn't click it when I clicked on submit nothing happened. Try opening in IE or rebooting your computer and trying again. Or maybe if you have adblock whitelisting that site?

sgdavies@hotmail.com
11-29-2017, 07:28 PM
Did you check the box that asks if you're a robot? I opened the page in Chrome and that robot thing wasn't there. Since I didn't see it, didn't know it was there and couldn't click it when I clicked on submit nothing happened. Try opening in IE or rebooting your computer and trying again. Or maybe if you have adblock whitelisting that site?

I been told it’s been deactivated while ftdna upgrade to hg38. I will wait till next year and try again. Thanks though.

Osiris
11-29-2017, 08:04 PM
Once I switched browsers and got the robot question I successfully requested my BAM on Nov 27. Got the response back that it will take 2 to 4 weeks for this to complete processing.

This was for an Aug order which never was HG19.

lgmayka
11-29-2017, 08:17 PM
This works for everyone in R1b-L151, which is P312 and U106.
Correction: R1b-L151 (https://yfull.com/tree/R-L151/) includes P312 and U106, but also S1200 (somewhat common), A8051 (rare), and A8039 (extremely rare). I don't know whether the expert R1b trees cover these other clades.

Mikewww
11-29-2017, 09:31 PM
Correction: R1b-L151[/URL] includes P312 and U106, but also S1200 (somewhat common), A8051 (rare), and A8039 (extremely rare). I don't know whether the expert R1b trees cover these other clades.

They will definitely take L151 folks of all kinds. It is particularly helpful on age estimates to have more deep branching subclades.

I don't think there is any reason to fear this. These folks have improved their automation so the processes are there. It's free so that can't be bad and they don't generally use BAM files so it is not the same thing as a BAM file interpretation.

Here is the actual upload instructions web page:

http://haplogroup-r.org/instructions.html

I've edited my original post so as not to give the wrong impression.

Wing Genealogist
11-29-2017, 11:11 PM
However, usually the Big Y Raw Results VCF/BED files are available almost immediately.

It had been my experience with the "old" Big Y results that the VCF/BED file typically appeared the day after the Big Y results are posted. I don't know if this still holds true or not.

Past experience has also shown where "rarely" the VCF/BED file didn't become available, and needed someone to contact FTDNA to fix the situation. Unfortunately, I do expect this will likely continue.

Mikewww
11-30-2017, 03:04 AM
It had been my experience with the "old" Big Y results that the VCF/BED file typically appeared the day after the Big Y results are posted. I don't know if this still holds true or not.
For L21 results I used to directly email and ask on the day of the posting. Generally, people almost all got back by the next day so it appears that VCF/BED files are available on the day of or the next morning. There doesn't appear to be any change although the GAP "Lab Results Received" report is lagging.

Just as a reminder, I asked FTDNA to add a project admin option to be notified by email when the Big Y results come in. I think that one is simple enough they'll do quickly.

rms2
01-06-2018, 09:30 PM
Aha! YFull's new tree, version 6.01, is up.

Here's the R1b part:

R1b Tree (https://www.yfull.com/tree/R1b/)

Nothing new for my bunch, but we can't get a BAM file for our latest guy to submit to YFull, and we still have three Big Y tests pending.

Wolds Wanderer
01-06-2018, 09:56 PM
I'm the same. I've now got three project members waiting to download their BAM files.