Big Y upgrade

General discussions regarding DNA and its uses in genealogy research

Posts: 2048
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Wed Jan 10, 2018 11:22 pm
Gioiello wrote:
dartraighe wrote:Gioello
I had a new Big Y match today. He has broken up the 23 SNP block of SNPs that I share with my first Big Y match. He is not a YSTR match and we have 26 mismatched SNPs. His most distant known ancestors are from Wales with a ancient Welsh surname. I am pleased that I am not in an SNP bottlenecked branch.


Glad to know that, but unfortunately without the Big Y and the YFull exam we lack many possibilities. Nothing is sure with the vcf file of FTDNA.


Gioiello
This a great YSNP match for me now that he sent me his 111 YSTR marker haplotype. He is a GD of 14 at 67 markers and 21 at 111 markers to my haplotype, but he has specific markers that define our dna subclade. He has several 67 marker matches with Welsh surnames and if we match in a lot of SNPs then they certainly match him also. I reckon that we had a common ancestor around 2,160 years ago.
Last edited by dartraighe on Sun Jan 14, 2018 5:36 pm, edited 1 time in total.

Posts: 2048
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Thu Jan 11, 2018 9:59 pm
FTDNA updated the tree today and I have 15 SNPs that my match does not have. This match has broken up my SNP block that I got from my Big Y test. The good thing about the Big Y test results is that an SNP match will show up that is not YSTR match. If a tester does not join a project he will still be added to your matches list as long as he is within the 30 YSNP threshold.

I have a GD of 14 at 67 YSTR markers and 15 SNP differences to the new Big Y tester who is one of an SNP cluster located in south Wales. My ancestor separated from this group around 2,160 ybp.

YSTR tests are history. YSNP tests are the way to go. Anyone who has the WAMH 67 or 111 could be in any one of a large number of subgroups. I have made more progress with two Big Y tests in the last two years than with YSTR tests in the nine years before that.
Last edited by dartraighe on Sat Jan 13, 2018 9:36 pm, edited 1 time in total.

Posts: 2048
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sat Jan 13, 2018 6:28 am
A great blog about the Big Y from Roberta Estes.
https://dna-explained.com/2018/01/12/wo ... ults-hg38/

"If you are a Family Tree DNA customer, and in particular, a male or manage male kits, you’re familiar with the Big Y test.

The Big Y test scans the entire gold standard region of the Y chromosome, hunting for mutations, called SNPs, that define your haplogroup with great precision. This test also discovers SNPs never before found. Those newly discovered SNPs may someday become new haplogroup branches as well. The Big Y test is how the Y DNA phylotree has been expanded from a few hundred locations a few years ago to more than 78,000, and along with that comes our understanding of the migration patterns of our ancestor."

Posts: 2048
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Tue Jan 16, 2018 1:58 pm
Due to the fact that I could not find 67 marker YSTR matches I kept myself interested by looking for SNP matches. The good thing about the Big Y test is that any tester who doesn't want to join projects or make his YSTR profile public will have no choice when his results come in. They will be posted to your page as long as the threshold is within 30 SNPs between the two matches. If I had been able to see my 25 marker matches YSTR profiles I would have contacted those with DYS492=13 because most of those were tested to 67 and 111 markers. They are not in any projects so I cannot see all of their YSTRs. FTDNA's 67 marker threshold is too rigid. My new Big Y match is a GD of 14 @67 and he was never going to show as a YSTR match within the FTDNA threshold for 67 markers.

A tester has to look at the origin place of the parent clades to try and get an idea of the pathway of their ancestors. I understand that some testers have different goals and they are confused with YSTR and YSNP labels. I think that YSTRs are a waste of money and time. YSTRs will point a tester in the right direction but at the end of the day a tester will have to SNP test to determine the dept of the relationship. I have 32 reliable SNP markers to work with now. YSTR markers are too volatile for my liking.

My goal from the outset was to try and find the path of my paternal ancestor into the Isles. Other testers are looking for YSTR matches with the same surname. I already know a lot of people with the same YSTR profile and the same surname. They are my cousins here in Ireland and elsewhere. If a tester with the same surname and within the 67 marker FTDNA threshold shows up, I will know if he is related or not because I have a good paper trail. And if he is not in my paper trail he will be taking a Big Y test to prove the relationship.

One poster asks "Is it possible to have a BigY match who is not also a 67 or 111 match?"

I posted a few days ago that my new Big Y match is a GD of 14 at 67 markers. I had to write to the new match and ask for the YSTRs.

FTDNA's maximum Big Y matching threshold is 30 SNPs between two testers, 15 each. Any tester who has a 15 SNPs difference will not show up as a 67 marker match because 15 SNPs are estimated to be around 1,500 to 2,000 years ybp. A 60/67 marker YSTR match could be within 700-1,000 ybp. It depends on which YSTR markers the differences are, the slow or fast mutating markers. YSTR matches are not all within the same time frame.

A tester who is a GD of 60/67 and has taken the Big Y will show in your matches but there will be Big Y matches that don't show in your YSTR matches. FTDNA needs to raise the threshold to 50 at least for my dna group. If they don't I will be missing matches in my terminal subgroup. I have 32 SNPs under my main subgroup status and if another tester shares only 10 of those 32 we will not be within the FTDNA threshold and he will not be on the FTDNA tree. FTDNA does not put a tester on the tree without a request from the admins. And if a Big Y tester outside the thresold is not in the projects he will be anonymous.
Last edited by dartraighe on Mon Jan 29, 2018 6:50 pm, edited 3 times in total.

Posts: 2048
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sun Jan 28, 2018 9:17 am
It is possible also for two testers who are within the FTDNA YSTR threshold of 7 @67 makers to not show up as Big Y matches because they are above the 30 SNP threshold. FTDNA could raise the threshold to 50 SNPs but that is alright in the short term. In the coming years we expect a lot more testers taking the Big Y test and our pages will be full of matches. We just need to be patient.

FTDNA shows five levels in my matches mini-tree and I certainly don't want matches from the first two upper levels at present. My pages would be full of SNP matches like before. The SNP group that I am interested in at present are those who have some of the SNPs that I picked up from my Big Y. I don't see any complaints from the M222 group.

When a tester gets his results from his Big Y, FTDNA does not name the SNPs that have passed their threshold limits and are deemed good quality SNPs. The FGC and Yfull teams are not shy about naming them. After a Big Y test there should be no such thing as an unnamed variant. You would think that they would be keen to claim SNPs found in their own tests.

Posts: 2048
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Wed Jan 31, 2018 7:25 pm
A poster wrote;
I myself have two 67-marker matches (at GD 7) who have taken the Big Y test. They do not appear on my Big Y Matches page.

Dr Iain,
"These cases rarely occur, but when they do, they happen to the same people. This can only happen when people have a significantly greater number of SNP mutations than average, a significantly smaller number of STR mutations than average, and matches in just the right locations who have the same thing.

At 67 markers, there is a sweet spot around 1340 years ago when 3% of BigY matches will be lost, but 0.4% of Y-67 matches will still be found, meaning that about 0.012% of matches will be found in Y-67 and not in BigY.

At 111 markers, the sweet spot is a little earlier (1160 years), and should apply to only around one in 75,000 matching pairs.

These numbers can be raised slightly if people have unusually high test coverage, if there is some problem with contamination in tests, or if there are back-mutating STRs. A situation may arise in a particular haplogroup where two common lines show fewer than average STR mutations and many SNP mutations, meaning that an entire haplogroup can be prone to this particular affliction, but is a rare phenomenon over all haplogroups and is not typical in R1b."

The counter situation, where BigY matches are missing from Y-67 and Y-111 tests, is very common. It should occur in 98% and 99.3% of matching pairs, respectively, in time periods of around 1200 years ago.

- Iain.

Posts: 2048
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Tue Feb 06, 2018 8:39 am
Yfull has upgraded my YSTR info. The Big Y test is a very good quality test and is the best price at present for an NGS test. A tester should get enough info from this test to establish his ancestral Y-line. My son is an exact match on all of the YSTR markers and YSNPs compared at Yfull.


YSTRs (all): 587
Reliable alleles: 529 (90.12%)
Uncertain alleles: 7 (1.19%)
N/A: 51 (8.69%)


Raw data
ChrY BAM file size: 0.62 GbHg19
Reads (all): 10039487
Mapped reads: 10039487 (100.00%)
Unmapped reads: 0
Length coverage: 15014197 bp (58.53%)
Min depth coverage: 1X
Max depth coverage: 7999X
Mean depth coverage: 76.78X
Median depth coverage: 55X
Length coverage for age: 8112832 bp
No call: 10639369 bp

Posts: 2285
Joined: Sun Mar 18, 2012 7:08 am
Location: Pisa (Italy)
YDNA:
R- Z2110 (KV7Y2)
MtDNA:
K1a1b1e/HQ176413
PostPosted: Tue Feb 06, 2018 8:46 am
dartraighe wrote:Yfull has upgraded my YSTR info. The Big Y test is a very good quality test and is the best price at present for an NGS test. A tester should get enough info from this test to establish his ancestral Y-line. My son is an exact match on all of the YSTR markers and YSNPs compared at Yfull.


YSTRs (all): 587
Reliable alleles: 529 (90.12%)
Uncertain alleles: 7 (1.19%)
N/A: 51 (8.69%)


Raw data
ChrY BAM file size: 0.62 GbHg19
Reads (all): 10039487
Mapped reads: 10039487 (100.00%)
Unmapped reads: 0
Length coverage: 15014197 bp (58.53%)
Min depth coverage: 1X
Max depth coverage: 7999X
Mean depth coverage: 76.78X
Median depth coverage: 55X
Length coverage for age: 8112832 bp
No call: 10639369 bp


But how many no calls got you and how many your son? It is unbelievable that you got the same no calls, which are about 20000 now, and how many important SNPs, private SNPs, may be into them?

Posts: 2048
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Tue Feb 06, 2018 12:29 pm
Gioiello wrote:
dartraighe wrote:Yfull has upgraded my YSTR info. The Big Y test is a very good quality test and is the best price at present for an NGS test. A tester should get enough info from this test to establish his ancestral Y-line. My son is an exact match on all of the YSTR markers and YSNPs compared at Yfull.


YSTRs (all): 587
Reliable alleles: 529 (90.12%)
Uncertain alleles: 7 (1.19%)
N/A: 51 (8.69%)


Raw data
ChrY BAM file size: 0.62 GbHg19
Reads (all): 10039487
Mapped reads: 10039487 (100.00%)
Unmapped reads: 0
Length coverage: 15014197 bp (58.53%)
Min depth coverage: 1X
Max depth coverage: 7999X
Mean depth coverage: 76.78X
Median depth coverage: 55X
Length coverage for age: 8112832 bp
No call: 10639369 bp


But how many no calls got you and how many your son? It is unbelievable that you got the same no calls, which are about 20000 now, and how many important SNPs, private SNPs, may be into them?


Gioiello
I am focused on the positives, not the negatives in my Big Y test and there is a lot of positive stuff , SNPs and YSTRs. If only I could find 20 testers who had some or most of my ancestral markers I would be pleased and finished too.

Posts: 2048
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sun Feb 11, 2018 11:50 am
Here's the YFULL data for one of YSEQ's new 30x WGS:

ChrY BAM file size: 0.45 GbHg38
Reads (all): 5656142
Mapped reads: 5642115 (99.75%)
Unmapped reads: 14027 (0.25%)
Length coverage: 26362675 bp (99.80%)
Min depth coverage: 1X
Max depth coverage: 8013X
Mean depth coverage: 26.90X
Median depth coverage: 15X
Length coverage for age: 8471482 bp
No call: 52368 bp

Known SNPs:
SNPs (all): 115346
Positive: 3004 (2.60%)
Negative: 112128 (97.21%)
Ambiguous: 193 (0.17%)
No call: 20 (0.02%)

STRs (all): 587
Reliable alleles: 539 (91.82%)
Uncertain alleles: 27 (4.60%)
N/A: 21 (3.58%)

Compared with my Big Y test.

Raw data
ChrY BAM file size: 0.62 GbHg19
Reads (all): 10039487
Mapped reads: 10039487 (100.00%)
Unmapped reads: 0
Length coverage: 15014197 bp (58.53%)
Min depth coverage: 1X
Max depth coverage: 7999X
Mean depth coverage: 76.78X
Median depth coverage: 55X
Length coverage for age: 8112832 bp
No call: 10639369 bp

SNPs (all): 115339
Positive: 2237 (1.94%)
Negative: 97183 (84.26%)
Ambiguous: 135 (0.12%)
No call: 15758 (13.66%)

YSTRs (all): 587
Reliable alleles: 529 (90.12%)
Uncertain alleles: 7 (1.19%)
N/A: 51 (8.69%)

The majority of no calls in my results are in the upstream levels of my branch. I can see this in my Yfull Y Report.
PreviousNext

Return to General DNA Discussion

Who is online

Users browsing this forum: No registered users and 1 guest

cron