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Robert McBride
02-16-2021, 06:31 PM
Yseq has a new WGS test for $399 with 400 base long reads!

Marmaduke
02-16-2021, 07:04 PM
More from Yseq: https://www.yseq.net/product_info.php?products_id=175886

Ibericus
02-16-2021, 07:04 PM
Very interesting. The stats they post seem better than what I got from my 30x Nebula WGS. I just can't find the number of reads they provide.

aaronbee2010
02-16-2021, 07:08 PM
Yseq has a new WGS test for $399 with 400 base long reads!

One of the YSEQ Facebook Admins (Y. Alzanama) made an announcement a while back regarding this test, but it's nice to see it available now. The statistics mentioned on the product page look very promising (particularly the improved Y-STR clarity vs 150bp reads).

Funnily enough, the Y-DNA Warehouse statistics page initially named this test something along the lines of DNBSEQ (YSEQ). I've downloaded a sample chrM BAM file from YSEQ's public FTP server and the read names clearly indicate that these are BGI DNBseq reads. The number of false mismatches per read are quite high but as these are random errors, they can be offset with sufficient coverage.

Robert McBride
02-16-2021, 07:19 PM
Funnily enough, the Y-DNA Warehouse statistics page initially named this test something along the lines of DNBSEQ (YSEQ). I've downloaded a sample chrM BAM file from YSEQ's public FTP server and the read name clearly indicates that these are BGI DNBseq reads. The number of false mismatches per read are quite high but as these are random errors, they can be offset with sufficient coverage.[/QUOTE]

Do you know if this type of test needs a lot of dna? With the previous yseq wgs you had to send them four sample brushes even if they already had your dna in storage .

JMcB
02-16-2021, 07:20 PM
Even though this would be redundant for me, I’m tempted!

aaronbee2010
02-16-2021, 07:23 PM
Do you know if this type of test needs a lot of dna? With the previous yseq wgs you had to send them four sample brushes even if they already had your dna in storage .

Someone asked more or less the same question on the YSEQ Facebook group and T. Krahn answered them with this reply:


We can use a standard YSEQ sample collection kit (2 brushes).

JMcB
02-16-2021, 07:24 PM
Do you know if this type of test needs a lot of dna? With the previous yseq wgs you had to send them four sample brushes even if they already had your dna in storage .

According to a question on their Facebook page, Thomas replied:

“We can use a standard YSEQ sample collection kit (2 brushes).”


Edit:

When asked if a customer could use a sample already stored at YSEQ, Thomas said:

“Generally, yes. If the sample fails the QC for some reason, we’ll use the backup brush or in the worst case, contact you for a new sample”.

MacUalraig
02-17-2021, 04:50 PM
My last three kits were all at 400bp, came in between Feb 4th and 7th. However I paid the full earlier price (e544.35) and now its cheaper!

dosas
02-17-2021, 05:17 PM
One of the YSEQ Facebook Admins (Y. Alzanama) made an announcement a while back regarding this test, but it's nice to see it available now. The statistics mentioned on the product page look very promising (particularly the improved Y-STR clarity vs 150bp reads).

Funnily enough, the Y-DNA Warehouse statistics page initially named this test something along the lines of DNBSEQ (YSEQ). I've downloaded a sample chrM BAM file from YSEQ's public FTP server and the read names clearly indicate that these are BGI DNBseq reads. The number of false mismatches per read are quite high but as these are random errors, they can be offset with sufficient coverage.

According to your personal opinion, would it be worth it to buy this over Nebula, for the extra price? I am planning to get one for my dad, soon.

Robert McBride
02-17-2021, 06:36 PM
My last three kits were all at 400bp, came in between Feb 4th and 7th. However I paid the full earlier price (e544.35) and now its cheaper!

How long did they take?
Its now saying “extracting b swab” next to my order so fingers crossed they can do the test without me having to send a new sample.

MacUalraig
02-17-2021, 06:59 PM
How long did they take?
Its now saying “extracting b swab” next to my order so fingers crossed they can do the test without me having to send a new sample.

Somewhat longer than the normal 5-6 weeks, but that was supposed to be a one-off hold up. I think the last of them took 8 weeks.
I also have another I only paid for earlier this month so hopefully that will be back to normal schedule.

losAntonis
02-24-2021, 10:56 AM
I ordered mine last sunday and am looking forward to the results to compare them with the other NGSs I did.

teepean47
03-02-2021, 07:45 PM
I just sent back my sample so the waiting has started.

ThaYamamoto
03-02-2021, 07:51 PM
Great price but any possibility of a sale?

Coldmountains
03-02-2021, 07:53 PM
My last three kits were all at 400bp, came in between Feb 4th and 7th. However I paid the full earlier price (e544.35) and now its cheaper!

You did the 400 bp 15x wgs test or the 50x like in the published test runs? I just wonder how the 15x wgs400 compares to a classical dante or nebula 30x

MacUalraig
03-02-2021, 08:01 PM
They were purchased and delivered at 15x WGS (~7x chrY).

aaronbee2010
03-03-2021, 04:41 PM
According to your personal opinion, would it be worth it to buy this over Nebula, for the extra price? I am planning to get one for my dad, soon.

I'm in the process of generating some simulated 15x WGS400 data (from the 50x WGS400 BAM from sample 16672) to analyse to see how well the 15x test that customers will actually receive performs compared to standard 30x WGS tests, although I'm busy with work at the moment and my health hasn't been the best recently so I can't give an ETA at the moment.

Regarding YSEQ's WGS400 test, their showcased statistics have been impressive but the BAM file used for these statistics has 50x mapped coverage whereas they're initially making the test available with 15x coverage (and possibly lower mapped coverage), so these statistics are almost certainly not entirely representative of what customers with 15x WGS400 data will receive and could even be considered as misleading to customers of the 15x product by some people.

The "Est. Years/SNP" metric on Y-DNA warehouse is similar for their standard 50x WGS (150 bp paired-end) test and the new 50x WGS400 (400 bp single-end), so when coverage is more-or-less controlled, the Y-SNP resolution appears to be similar (although we only have one WGS400 sample on there at the moment). This suggests that increased read length doesn't contribute much to Y-SNP coverage so carrying this thought forward, the WGS400 15x test that a consumer would end up purchasing from YSEQ would probably have a similar "Est. Years/SNP" to the 150 bp 15x WGS from YSEQ, which gets outperformed by Nebula and Dante 30x WGS tests for Y-SNP discovery (at least going by this admittedly heuristic metric).

Having said this, even YSEQ have mentioned that one of the main advantages of 400 bp read lengths would be increased Y-STR resolution, but the results we've seen here are with 50x coverage and not 15x, so the "real" Y-STR resolution of this test remains to be seen. The problem here is that the ability of reads with a higher length to span repeat regions in their entirety can be easily negated by lower coverage, so it's hard to guess which test will be better. I'm not sure what the best STR test to perform on my simulated 15x data is though, so I'm currently at a crossroads at the moment. Any recommendations here from anyone would be appreciated. I've currently got the BAM Analysis Kit in mind, although I think this uses lobSTR, which uses an Illumina PCR stutter model, so I'm not sure how well this model will work for DNBSEQ data. Even screenshots of Y-STRs in IGV showing both 15x and 50x BAM files is better than nothing.

TL;DR: Y-SNP resolution for the WGS400 test is probably worse than Nebula or Dante tests (assuming the latter company provides a file that isn't undersequenced or has excessive microbial contamination). Y-STR resolution for this test when comparing 15x WGS400 data (~7x chrY coverage) to 30x 150 bp WGS (~15x chrY coverage) currently remains to be seen, although I'm figuring this out. Until this is figured out, it's hard to say whether or not the extra $80 is worth it.

Northern Adriatic
03-07-2021, 02:11 PM
I know that this could sound like a newbie question (and I am a newbie) but... is this better or worse than BIG Y 700?
The goal in my case is just to find out my subclades (which looking at 23andme raw data were all negative except for I-Z139 which was "not determined" but with I-Z138 negative) and therefore possibly the origins of my I1 haplogroup.
I would take the autosomal and mtdna part as a nice bonus, since judging from Admixture Studio the genotype ratio of my 23andme v5 test is in the range of 25-30%.

Dave-V
03-08-2021, 03:43 PM
I know that this could sound like a newbie question (and I am a newbie) but... is this better or worse than BIG Y 700?

Hard to say. On the clear positive side, the YSEQ WGS test is cheaper than Big Y700 and includes autosomal and mtdna.

They are not identical but probably close to equivalent if your purpose is just finding where you fall on the Y-DNA haplotree down to present day since they will both give you nearly the same trail of SNPs down to present day. The YSEQ 15x test has on average a fraction less coverage than the Big Y, their 50x test seems to have a fraction more coverage. But the differences in company practices probably have more impact on whether any given SNP that might be important to you is reported or missed in your test. It appears to me from repeated observation that FTDNA's aligner has stricter quality criteria than WGS aligners which results in fewer SNPs reported during alignment, but I do know that typically FTDNA reports SNPs from regions of the Y chromosome that YFull (the main interpreter of WGS tests) marks as low quality, so either way small variances in SNP reporting can occur just based on differences in how the tests are interpreted. Which test is better in that sense depends more on the element of chance and where your important SNPs sit and how many reads they had in your test.

Because of their larger tester database, the FTDNA haplotree has better definition than the YFull haplotree especially in heavily-tested haplogroups like I and R, so you'd probably get placed in a subclade closer to present day on the FTDNA haplotree. But if you don't mind doing that analysis manually by comparing your WGS data to the FTDNA public haplotree you can see where you fall there so that's not really a show-stopper in my opinion.

Again more of a factor in the heavily-tested haplogroups like I and R, but FTDNA has the larger match database which would be necessary if you want to use the information for genealogy purposes rather than only find your closest subclade. But of course if you happen to fall into a group that has also invested heavily in WGS that's less of a concern, so if you suspect that you'll fall into a certain haplogroup it's worth checking it out on the YFull haplotree to see how many testers are there compared to the FTDNA tree, which can give you a perspective on the relative value to you of the larger FTDNA match database.

So in my opinion if you don't have a good sense of your haplogroup already then the main differences are cost and autosomal/mtdna versus the larger match database and I would go for whichever of those is the more attractive add-on.

Northern Adriatic
03-08-2021, 04:51 PM
Thanks a lot Dave! At the end of all, my main goal is to find out more about the history of my patrilinear side through finding the right subclade. As I said, 23andme and all the websites I've uploaded its raw data on (e.g. morley, yseq itself) give me I-Z58 as a result because I tested "negative" for both I-Z59 (and subclades, except for one not determined) and I-Z138 (but I-Z139 is not determined). I suspect a possible basal I-Z58* outcome or, possibly, a new subclade under I-Z58 (or a pre I-Z139?), if 23andme was right about its calls. I am not sure which one could be better for the specific situation.

I've decided to dig more as I1 is not a super common haplogroup in my country (Italy, even more considering that it comes not from my north-east side but from my central-southern side) and I've thought it would be worthy to investigate more. I will try to figure out which test is the best. Price is not a huge issue, although I don't want to overpay for something which in 4-5 years might be surpassed by an even more accurate test.

Autosomal gives me a bit of curiosity because with the 23andme raw data I tend to plot mostly with the Southern Balkan cluster (Thessaly, Albania) and who knows maybe a more accurate report with a higher genotype ratio would confirm or fix that. Who knows though, maybe the genotype ratio would remain the same and it is better to wait for science to progress for another autosomal test. It would still be a nice side bonus.

Your answer was super helpful though! Thanks!

MacUalraig
03-09-2021, 03:43 PM
Hard to say. On the clear positive side, the YSEQ WGS test is cheaper than Big Y700 and includes autosomal and mtdna.



You forgot to mention it comes with the BAM file included in the price. That's USD100 extra at the other firm.

ChrisR
04-02-2021, 12:39 PM
It seems to be rather quiet about the YSEQ WGS400 $399 test?
I wait for the analysis reports (possibly including YFull) of 2-3 independent researchers, since I would like to recommend it to a friend after understanding what is delivered especially naturally for the Y. Or if going with a conventional WGS test (likely the YSEQ 15x 45Gb or 30x 90Gb) would be better.
Is there another place with ongoing discussion of new results?

Robert McBride
04-02-2021, 01:44 PM
It seems to be rather quiet about the YSEQ WGS400 $399 test?
I wait for the analysis reports (possibly including YFull) of 2-3 independent researchers, since I would like to recommend it to a friend after understanding what is delivered especially naturally for the Y. Or if going with a conventional WGS test (likely the YSEQ x15 45Gb or x30 90Gb) would be better.
I there another place with ongoing discussion of new results?

I ordered it on the same day it became officially available (16th Feb) and the results are still pending.
As soon as they are ready and yfull has finished analysing them I will post the statistics alongside the ones for my 50x WGS for you to compare.

teepean47
04-02-2021, 06:47 PM
I ordered it on the same day it became officially available (16th Feb) and the results are still pending.
As soon as they are ready and yfull has finished analysing them I will post the statistics alongside the ones for my 50x WGS for you to compare.

Same here. Processing started 03/09/2021 so it will take a while.

losAntonis
04-02-2021, 08:29 PM
It seems to be rather quiet about the YSEQ WGS400 $399 test?
I wait for the analysis reports (possibly including YFull) of 2-3 independent researchers, since I would like to recommend it to a friend after understanding what is delivered especially naturally for the Y. Or if going with a conventional WGS test (likely the YSEQ 15x 45Gb or 30x 90Gb) would be better.
Is there another place with ongoing discussion of new results?

The conventional WGS test at YSEQ aren't available anymore.
The WGS400 for $399 is a 15x WGS.
My test is running and I will report after results are finished.

randalgibbs
04-03-2021, 03:23 AM
The conventional WGS test at YSEQ aren't available anymore.
The WGS400 for $399 is a 15x WGS.
My test is running and I will report after results are finished.

The conventional WGS tests are still for sale on the website.
https://www.yseq.net/index.php?cPath=29

losAntonis
04-03-2021, 05:32 AM
The conventional WGS tests are still for sale on the website.
https://www.yseq.net/index.php?cPath=29

Thomas Kran wrote on Facebook, that YSEQ doesn't sell them anymore. They are still there in the list for the backlog tests.

randalgibbs
04-03-2021, 03:00 PM
Thomas Kran wrote on Facebook, that YSEQ doesn't sell them anymore. They are still there in the list for the backlog tests.

That makes sense as I don't know why anyone would pay $599 for the old 15x, when you can get longer reads for $399. I wonder if they will be adding 30x and 50x versions of the WGS400 test.

aaronbee2010
04-03-2021, 03:16 PM
That makes sense as I don't know why anyone would pay $599 for the old 15x, when you can get longer reads for $399. I wonder if they will be adding 30x and 50x versions of the WGS400 test.

I asked this to one of the YSEQ co-owners and he replied with this:


We may offer higher coverage versions in the future, but for now we try to serve as many customers as fast as possible.

MacUalraig
04-03-2021, 04:38 PM
I asked this to one of the YSEQ co-owners and he replied with this:

My only concern is that the old CeGaT service was very fast and impatience is my middle name. So lets hope the new venture beds in and gets up to that kind of turnaround...

losAntonis
04-03-2021, 04:42 PM
My only concern is that the old CeGaT service was very fast and impatience is my middle name. So lets hope the new venture beds in and gets up to that kind of turnaround...

I always say "The waiting time is the most exciting time of DNA testing".
Unfortunately, after the results are ready, waiting goes on.

MacUalraig
04-03-2021, 04:47 PM
I always say "The waiting time is the most exciting time of DNA testing".
Unfortunately, after the results are ready, waiting goes on.

44133

I'm not a big user of STRs these days but I'm still curious to see if YFull come up with a better dataset than with the old test. zzzzz

Ibericus
04-03-2021, 05:02 PM
44133

I'm not a big user of STRs these days but I'm still curious to see if YFull come up with a better dataset than with the old test. zzzzz

They should do a "pick 30 STRs" kind of panel to fill the gaps left by most WGS tests.

losAntonis
04-03-2021, 05:04 PM
My only concern is that the old CeGaT service was very fast and impatience is my middle name. So lets hope the new venture beds in and gets up to that kind of turnaround...

I ordered my test at 22 February and one week ago Thomas told me, that the batch of my test is at the sequencer.

aaronbee2010
04-03-2021, 07:19 PM
My only concern is that the old CeGaT service was very fast and impatience is my middle name. So lets hope the new venture beds in and gets up to that kind of turnaround...

The administrator of the H600 project asked a few questions to the co-owner I previously mentioned and was apparently told by said co-owner that YSEQ do the sequencing for their WGS400 in-house. The exact degree of the time improvement by cutting out the middleman (CeGaT in this case) remains to be seen though.

MacUalraig
04-03-2021, 07:39 PM
The administrator of the H600 project asked a few questions to the co-owner I previously mentioned and was apparently told by said co-owner that YSEQ do the sequencing for their WGS400 in-house. The exact degree of the time improvement by cutting out the middleman (CeGaT in this case) remains to be seen though.

I suspected that was the case based on various hints/clues. Not sure it translates to faster though - depends on how big the batches are. The old service had a sort of agreement to run no slower than once every 2 months.

ChrisR
04-06-2021, 07:23 PM
I asked this to one of the YSEQ co-owners and he replied with this:

We may offer higher coverage versions in the future, but for now we try to serve as many customers as fast as possible.
I asked that in the Fb YSEQ group and there Thomas answered (https://www.facebook.com/groups/YSEQDNA/permalink/3724016451010725/?comment_id=3724308867648150):

Our goal was to be able to serve as many customers as possible during the launch phase to require the shortest possible processing time. However we'll soon make higher coverage WGS400 versions available.
Hopefully a 30x version will be available soon as I think having ~15x on the Y is something every serious Y-DNA researcher wants to have at least the option for, ~7x feels like 1000 Genomes data from ages ago (I know other things also count).


They should do a "pick 30 STRs" kind of panel to fill the gaps left by most WGS tests.
That seems like a very good idea to me also for YSEQ. Has someone asked Thomas/Astrid regarding this? Maybe 15/18 STRs would be also enough if the "custom setup" is substantially more costly then the standard panels.

Coldmountains
04-13-2021, 07:42 AM
I ordered my test at 22 February and one week ago Thomas told me, that the batch of my test is at the sequencer.

How long does it usually take after this stage to get the results?

losAntonis
04-13-2021, 09:23 AM
How long does it usually take after this stage to get the results?

I don't know. Even Thomas doesn't has an accurate answer, yet.
I am not in hurry, since it is just an upgrade for me.

MacUalraig
04-13-2021, 10:29 AM
The kit I paid for on Feb 4th returned results on Apr 9th. However I should mention that I placed two new orders on Apr 6th and 7th so those events may not be unconnected ;-)

ChrisR
04-14-2021, 01:04 PM
Hopefully a 30x version will be available soon as I think having ~15x on the Y is something every serious Y-DNA researcher wants to have at least the option for, ~7x feels like 1000 Genomes data from ages ago (I know other things also count).
Astrid answered to an email question that it is possible to order a 30x 90Gb WGS400, instead of the standard 15x 45Gb for $399 (https://www.yseq.net/product_info.php?products_id=175886) for double the price. Unfortunately on the website there is no mention of the read depth or GBases.

MacUalraig
04-14-2021, 05:12 PM
Astrid answered to an email question that it is possible to order a 30x 90Gb WGS400, instead of the standard 15x 45Gb for $399 (https://www.yseq.net/product_info.php?products_id=175886) for almost double the price. Unfortunately on the website there is no mention of the read depth or GBases.

Yes they should tidy the page up and there is the issue of the non-standard sample stats too.

rock
04-15-2021, 12:54 PM
sattistics of WGS400, not bad.
44336

aaronbee2010
04-15-2021, 01:22 PM
sattistics of WGS400, not bad.
44336

Slightly undersequenced according to YSEQ's criterion for the amount of sequencing data generated (45+ GBases) but the percentage of reads mapping to the reference genome is very impressive. Congratulations :)

ChrisR
04-17-2021, 05:53 PM
thanks @rock . The most interesting for me will be the Y-Stats and specifically those at YFull:
SNPs (Positive, No call), STRs (Reliable, N/A).

I would need to do updated comparisons but think the following DL result could be a reference:
3000 or more positive SNPs, under 400 no call, 600 or more Reliable STRs, less then 200 STRs N/A

Or this BigY500:
2200 or more positive SNPs, under 4000 no call, 700 or more Reliable STRs, less then 100 STRs N/A

MacUalraig
04-17-2021, 07:44 PM
thanks @rock . The most interesting for me will be the Y-Stats and specifically those at YFull:
SNPs (Positive, No call), STRs (Reliable, N/A).

I would need to do updated comparisons but think the following DL result could be a reference:
3000 or more positive SNPs, under 400 no call, 600 or more Reliable STRs, less then 200 STRs N/A

Or this BigY500:
2200 or more positive SNPs, under 4000 no call, 700 or more Reliable STRs, less then 100 STRs N/A

This just completed STR analysis (took 2 months+ at YFull)
ChrY BAM file size: 0.25 GbHg38
Reads (all): 845288
Mapped reads: 845288(100.00%)
Unmapped reads: 0
Length coverage: 23499477 bp(99.42%)
Min depth coverage: 1X
Max depth coverage: 724X
Mean depth coverage: 8.52X
Median depth coverage: 7X
Length coverage for age*: 8058353 bp
No call: 136878 bp

SNPs (all): 219497
Positive: 3009 (1.37%)
Negative: 15358 (7.00%)
Ambiguous: 56 (0.03%)
No call: 94 (0.04%)

STRs (all): 780
Reliable alleles: 597 (76.54%)
Uncertain alleles: 52 (6.67%)
N/A: 131 (16.79%)

MacUalraig
04-17-2021, 07:49 PM
The other one wasn't as good, the read depth is sub-par and so in particular are the STRs

ChrY BAM file size: 0.17 GbHg38
Reads (all): 575395
Mapped reads: 575395(100.00%)
Unmapped reads: 0
Length coverage: 23261753 bp(98.42%)
Min depth coverage: 1X
Max depth coverage: 692X
Mean depth coverage: 6.09X
Median depth coverage: 5X
Length coverage for age*: 7103744 bp
No call: 374602 bp

SNPs (all): 219497
Positive: 3005 (1.37%)
Negative: 15364 (7.00%)
Ambiguous: 74 (0.03%)
No call: 299 (0.14%)


STRs (all): 780
Reliable alleles: 510 (65.38%)
Uncertain alleles: 27 (3.46%)
N/A: 243 (31.15%)

Dalluin
04-18-2021, 11:23 PM
What software would you recommend to read the NGS BAM file?

Dalluin
04-18-2021, 11:25 PM
sattistics of WGS400, not bad.
44336

With what software do you output these statistics, please ?

rock
04-19-2021, 12:57 AM
With what software do you output these statistics, please ?

https://qual.iobio.io/

Northern Adriatic
04-19-2021, 07:49 PM
Sorry if the question sound stupid but I am trying to understand the statistics posted and I am still a bit confused.
On the Y-DNA, does this prove it to be as good as BIG Y 700 (excluding other factors such as mtdna + whole genome + price + bam file)?

aaronbee2010
04-20-2021, 08:42 PM
Here's (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254273/) a snippet from Press et al. The overdue promise of short tandem repeat variation for heritability which shows the authors predicted relationship between genome-wide coverage and expected coverage for reads fully spanning an STR plus 8 bp of flanking sequence on each side - genome-wide coverage and read length being the controllable variables here:


To accurately map an STR sequence read and retrieve its unit number genotype, the sequence read must span the STR of interest and include some unique flanking sequence. This requirement limits the length of STRs that can be accurately genotyped and decreases effective STR coverage compared to average whole-genome-sequencing coverage (Figure 2). For this reason, much of the existing sequencing data, which consists largely of short reads (36 bp, 50 bp, or 76 bp) with only modest genome coverage (5–20×) is not suitable for accurate, genome-wide calls of STR genotypes; only a fraction of STRs, mostly short ones, can be assessed with some confidence (Figure 2).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254273/bin/nihms626691f2.jpg

Figure 2: Effective reduction in STR coverage in whole-genome sequencing

Expected coverage of STRs for various sequencing depths and read lengths. We assumed 8 bp of flanking sequence on either side (per requirement for LobSTR software [38]). Black bars indicate nominal sequencing coverage for each scenario. 4–5× coverage (left panel) is typical for genomes in the human 1000 Genomes Project [95]; 15–20– coverage is typical for genomes in the A. thaliana 1001 Genomes Project [97,98].

While this is based on theoretical calculations, I think it does a decent job of showing that both depth of coverage and read depth are important for resolving Y-STRs. It would've been nice if they included the formula they used to generate those plots though.

It appears that with the 15x WGS400 test, the benefits of longer read length are negated by a lower number of reads fully spanning the Y-STR regions (plus flanking sequences).

randalgibbs
04-21-2021, 01:45 AM
Here's (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254273/) a snippet from Press et al. The overdue promise of short tandem repeat variation for heritability which shows the authors predicted relationship between genome-wide coverage and expected coverage for reads fully spanning an STR plus 8 bp of flanking sequence on each side - genome-wide coverage and read length being the controllable variables here:



While this is based on theoretical calculations, I think it does a decent job of showing that both depth of coverage and read depth are important for resolving Y-STRs. It would've been nice if they included the formula they used to generate those plots though.

It appears that with the 15x WGS400 test, the benefits of longer read length are negated by a lower number of reads fully spanning the Y-STR regions (plus flanking sequences).

My guess at the formula would be: (coverage) x (read length - (str length + 16)) / (read length). If I plot that formula for 30x coverage, my graph looks just like theirs. 44412

randalgibbs
04-21-2021, 05:20 AM
Using the formula I posited above, the plot of theoretical coverage of a 100bp 30x, 150bp 30x and 400bp 15x test is interesting. At least theoretically, the STR length at which a 400bp 15x test coverage exceeds the 150bp 30x test is about 78bp.44422

JamesKane
06-26-2021, 04:24 PM
Sorry if the question sound stupid but I am trying to understand the statistics posted and I am still a bit confused.
On the Y-DNA, does this prove it to be as good as BIG Y 700 (excluding other factors such as mtdna + whole genome + price + bam file)?

The production results received by the Y-DNA Warehouse are variable, but it seems YSEQ is targeting a 15x coverage at the current price point. You wind up with about 1 million fewer bases with 4 or more well aligned reads than BY700. On the other hand you wind up with 99.3% of the total Y chromosome covered with at least a single read vs. Big Y's 97%.

Personally, I'd go with WGS400 for the longer fragments. If you need to get more depth later on to shore up the other 1 million bases, you can always order another one and have YSEQ merge the BAMs.

If you need FTDNA's tree though, you really only have one choice.

Northern Adriatic
08-16-2021, 01:42 PM
The production results received by the Y-DNA Warehouse are variable, but it seems YSEQ is targeting a 15x coverage at the current price point. You wind up with about 1 million fewer bases with 4 or more well aligned reads than BY700. On the other hand you wind up with 99.3% of the total Y chromosome covered with at least a single read vs. Big Y's 97%.

Personally, I'd go with WGS400 for the longer fragments. If you need to get more depth later on to shore up the other 1 million bases, you can always order another one and have YSEQ merge the BAMs.

If you need FTDNA's tree though, you really only have one choice.
Thanks a lot! I've just ordered it, I will for sure bother you all more once I get my results! :)

capsian
08-26-2021, 12:08 AM
hello i want ask about the file healthy is it accurate or not?

Alfa
09-01-2021, 08:14 AM
Do you know if YSEQ cover both Mtdna and autosomal dna as well. If yes, do the YSEQ autosomal provide you with a much better coverage VS AncestryDNA/23andme?

I would love to try it.

Alfa
09-01-2021, 08:16 AM
The production results received by the Y-DNA Warehouse are variable, but it seems YSEQ is targeting a 15x coverage at the current price point. You wind up with about 1 million fewer bases with 4 or more well aligned reads than BY700. On the other hand you wind up with 99.3% of the total Y chromosome covered with at least a single read vs. Big Y's 97%.

Personally, I'd go with WGS400 for the longer fragments. If you need to get more depth later on to shore up the other 1 million bases, you can always order another one and have YSEQ merge the BAMs.

If you need FTDNA's tree though, you really only have one choice.



@JamesKane

Do you know if YSEQ cover both Mtdna and autosomal dna as well. If yes, do the YSEQ autosomal provide you with a much better coverage VS AncestryDNA/23andme?

I would love to try it.

MacUalraig
09-01-2021, 03:18 PM
@JamesKane

Do you know if YSEQ cover both Mtdna and autosomal dna as well. If yes, do the YSEQ autosomal provide you with a much better coverage VS AncestryDNA/23andme?

I would love to try it.

The WGS400 covers the whole genome (autosomes and sex chromosomes) and mitogenome. So yes its coverage is superior to Ancestry/23andMe. 3bn bases v 6-700k.

capsian
09-01-2021, 10:30 PM
The WGS400 covers the whole genome (autosomes and sex chromosomes) and mitogenome. So yes its coverage is superior to Ancestry/23andMe. 3bn bases v 6-700k.

I heard that cant transfer your result (i mean BAM autosomal WGS400) to FTDNA

MacUalraig
09-02-2021, 11:38 AM
I heard that cant transfer your result (i mean BAM autosomal WGS400) to FTDNA

Normally one transfers the Y and mt to YFull which has customers from all the sequencing companies including ftdna and autosomal to GEDMatch. No company is using the entire (autosomal) genome for matching. You can also have your Y displayed by the ytree/data warehouse team which has many ftdna kits on it but they don't have a matching/messaging system like YFull does.

capsian
09-02-2021, 02:04 PM
Normally one transfers the Y and mt to YFull which has customers from all the sequencing companies including ftdna and autosomal to GEDMatch. No company is using the entire (autosomal) genome for matching. You can also have your Y displayed by the ytree/data warehouse team which has many ftdna kits on it but they don't have a matching/messaging system like YFull does.

when my result exiting i will ask you how i will did this thanks you

JMcB
09-02-2021, 03:13 PM
when my result exiting i will ask you how i will did this thanks you


If you’ve tested at YSEQ they’ll be able to handle it for you. If I remember correctly, they’ll upload your Y & mtDNA results to YFUll and they’ll make a usable autosomal file for uploading to places like FTDNA & My Heritage. They may charge a modest fee for those services but I’m not sure what it is, if at all. So I would ask them about all of the above.

capsian
09-02-2021, 03:17 PM
If you’ve tested at YSEQ they’ll be able to handle it for you. If I remember correctly, they’ll upload your Y & mtDNA results to YFUll and they’ll make a usable autosomal file for uploading to places like FTDNA & My Heritage. They may charge a modest fee for those services but I’m not sure what it is, if at all. So I would ask them about all of the above.

thank you

MacUalraig
09-02-2021, 04:27 PM
If you’ve tested at YSEQ they’ll be able to handle it for you. If I remember correctly, they’ll upload your Y & mtDNA results to YFUll and they’ll make a usable autosomal file for uploading to places like FTDNA & My Heritage. They may charge a modest fee for those services but I’m not sure what it is, if at all. So I would ask them about all of the above.

Currently the results instructions include this:
"If you want to release your BAM files to YFull you can simply join the YFull group at YSEQ:
https://www.yseq.net/yfull_group.php"

although I still do it manually myself.

capsian
09-03-2021, 10:42 AM
Currently the results instructions include this:
"If you want to release your BAM files to YFull you can simply join the YFull group at YSEQ:
https://www.yseq.net/yfull_group.php"

although I still do it manually myself.

Hello link is not found

JamesKane
09-03-2021, 10:47 AM
Hello link is not found

The links to join YFULL's project is on the main YSEQ landing page near the middle under the Clade Finder and Haplogroup Predictor. You need to be logged into your account to access the link.

capsian
09-03-2021, 10:48 AM
The links to join YFULL's project is on the main YSEQ landing page near the middle under the Clade Finder and Haplogroup Predictor. You need to be logged into your account to access the link.

thanks you

capsian
09-03-2021, 04:31 PM
Hello i saw on twitter in page (
Y-DNA Sequencing in Syria ) new service about Autosomal DNA how ethnic groups and matches relativesresult for WGS400
in fact i dont know fact this post
here link https://twitter.com/DnaSyria/status/1433343920818298886

capsian
09-05-2021, 09:23 PM
Hello i saw on twitter in page (
Y-DNA Sequencing in Syria ) new service about Autosomal DNA how ethnic groups and matches relativesresult for WGS400
in fact i dont know fact this post
here link https://twitter.com/DnaSyria/status/1433343920818298886

i asked about this and news is true

Biharguy
09-17-2021, 06:42 PM
What is the current turnaround time for the WGS400?

capsian
09-18-2021, 04:46 PM
What is the current turnaround time for the WGS400?

2months

peloponnesian
09-21-2021, 09:43 AM
What is the current turnaround time for the WGS400?

They told me 3 months and they already had my sample in storage so YMMV.

sirdan
09-21-2021, 09:48 AM
2 months is desirable time. Now its 5 months or over it.

Biharguy
09-21-2021, 04:18 PM
Oh man. :/ Yeah they had the sample in storage too. I hope it is actually 3 months and not 5.

capsian
09-23-2021, 11:38 AM
Oh man. :/ Yeah they had the sample in storage too. I hope it is actually 3 months and not 5.

i hope this also

capsian
09-23-2021, 11:42 AM
They told me 3 months and they already had my sample in storage so YMMV.

they told you a 3 months u result will exiting
so i think 3 months not long

capsian
09-24-2021, 01:59 PM
Oh man. :/ Yeah they had the sample in storage too. I hope it is actually 3 months and not 5.

i know many friends tested their Yseq WGS400 and they are waiting for exiting result btw 3-4 months

capsian
11-02-2021, 08:31 PM
2 months is desirable time. Now its 5 months or over it.

5 months this mean your sample have problem example WGS-LIBC under average

aaronbee2010
11-03-2021, 12:16 AM
Here's a waiting time (weeks) histogram that T. Krahn of YSEQ has collected for the last WGS400 batch as of October 18th:

https://i.gyazo.com/2f6c3b599c314481c41e9dc45b2a6c6e.jpg

capsian
11-03-2021, 04:56 PM
Here's a waiting time (weeks) histogram that T. Krahn of YSEQ has collected for the last WGS400 batch as of October 18th:

https://i.gyazo.com/2f6c3b599c314481c41e9dc45b2a6c6e.jpg

21 week i think this samples have problem example WGS-LIBC under average

aaronbee2010
11-03-2021, 05:23 PM
21 week i think this samples have problem example WGS-LIBC under average

I've never heard of the term "WGS-LIBC" before, and I couldn't find any mention of it with a Google search. What does this term mean exactly?

capsian
11-03-2021, 05:55 PM
I've never heard of the term "WGS-LIBC" before, and I couldn't find any mention of it with a Google search. What does this term mean exactly?

it is mean concentration DNA

Biharguy
11-12-2021, 04:42 PM
Anyone received their WGS 400 results recently?

Biharguy
11-15-2021, 04:54 PM
Update on the WGS400. I emailed YSEQ and they told me that they have my raw data ready but they need to analyze the results still. They will start doing this after 2 weeks because of the customer backlog. So I'm expecting results in another month or mid December. I'm on month three at the moment.

capsian
11-19-2021, 02:06 PM
Anyone received their WGS 400 results recently?

yes just today

Biharguy
11-19-2021, 02:38 PM
yes just today

Exactly how long were you waiting for results? As well can you give some sample screenshots of how they interpreted your STR's, SNP's etc?

teepean47
11-19-2021, 07:34 PM
There's going to be a 50x WGS400 in the future. Couple of tests showed up at the Y-DNA Warehouse the other day.

https://ydna-warehouse.org/benchmarks

aaronbee2010
11-19-2021, 09:28 PM
There's going to be a 50x WGS400 in the future. Couple of tests showed up at the Y-DNA Warehouse the other day.

https://ydna-warehouse.org/benchmarks

I think those two submissions are the WGS400 datasets available on YSEQs public FTP server, but only JamesKane can confirm this.

teepean47
11-19-2021, 09:52 PM
I think those two submissions are the WGS400 datasets available on YSEQs public FTP server, but only JamesKane can confirm this.

Seems to be the case. I asked Thomas what the timeline might be.

"The one's you are asking about are the BETA runs of the currently advertised test at YSEQ."

"I believe it's on their product development road map but there are some obstacles that need to be cleared from the timeline. It should be a very fine option when it comes."

capsian
11-20-2021, 11:31 PM
Exactly how long were you waiting for results? As well can you give some sample screenshots of how they interpreted your STR's, SNP's etc?

Hi i m waiting 92 days
I have 11 SNP Novel in YSEQ ans 22 in yfull and str i not find in YSEQ
Here Quality my sample
47518
47519

karwiso
11-21-2021, 06:25 PM
Hi i m waiting 92 days
I have 11 SNP Novel in YSEQ ans 22 in yfull and str i not find in YSEQ
Here Quality my sample ...

I suggest that you upload your results to YFull. Join YFull group at YSEQ or upload via YFull's site: https://yfull.com/ If you do it via YSEQ then the analysis will cost 45$.
11x coverage for Y chromosome is quite ok/good. When analysis is done, then you can see your YFull report and statistics for Y chromosome BAM-file (like length coverage, median coverage, min/max).
You will also get your sublade/haplogroup on their tree: https://www.yfull.com/live/tree/E-Y141637/.
Probably you are already there since there are a couple of results from YSEQ.

capsian
11-23-2021, 03:35 PM
I suggest that you upload your results to YFull. Join YFull group at YSEQ or upload via YFull's site: https://yfull.com/ If you do it via YSEQ then the analysis will cost 45$.
11x coverage for Y chromosome is quite ok/good. When analysis is done, then you can see your YFull report and statistics for Y chromosome BAM-file (like length coverage, median coverage, min/max).
You will also get your sublade/haplogroup on their tree: https://www.yfull.com/live/tree/E-Y141637/.
Probably you are already there since there are a couple of results from YSEQ.

Hello Karwiso already I have upload my result to yfull and my sample it s YF94042
i formed new branch A30032
https://www.yfull.com/live/tree/E-A30032/
Thanks

capsian
11-23-2021, 03:43 PM
I suggest that you upload your results to YFull. Join YFull group at YSEQ or upload via YFull's site: https://yfull.com/ If you do it via YSEQ then the analysis will cost 45$.
11x coverage for Y chromosome is quite ok/good. When analysis is done, then you can see your YFull report and statistics for Y chromosome BAM-file (like length coverage, median coverage, min/max).
You will also get your sublade/haplogroup on their tree: https://www.yfull.com/live/tree/E-Y141637/.
Probably you are already there since there are a couple of results from YSEQ.


Here Report Yfull it seems good
47547

Biharguy
11-30-2021, 09:04 PM
I got the results from the WGS400 and uploaded to YFull. The depth coverage is much lower then the Big Y 700 but length coverage is much more then the Y700. I found that quite interesting. Which is better for finding more private variants?

MacUalraig
12-02-2021, 04:04 PM
I got the results from the WGS400 and uploaded to YFull. The depth coverage is much lower then the Big Y 700 but length coverage is much more then the Y700. I found that quite interesting. Which is better for finding more private variants?

It's an excellent question. My view is that breadth counts more than depth as long as you hit a minimum value which virtually all tests do anyway. To give an idea of what that min value might be, when I first started experimenting with low pass WGS in 2015 I was trying 2x v 4x and at that level you were definitely missing SNPs you needed i.e. getting no-calls (zero reads). The 15x that YSEQ sells combined with a bad sample can drop you down to maybe 4-5x for Y calls and you can be getting into unsafe waters then. I had one in the other day which had this:

Mean depth coverage: 5.52X
Median depth coverage: 4X

Known SNPs:
No call: 500 (0.19%)

But the next one at the same purchased test level got this:
Mean depth coverage: 11.21X
Median depth coverage: 9X

Known SNPs:
No call: 80 (0.03%)

80 no calls is still on the high side, I've had tests where it was down in single digits but big improvement.

Northern Adriatic
12-02-2021, 09:18 PM
I have not received an email with the results but I've just logged in the website and on "My Allele Results" I've got this:

Most specific position on the YFull YTree is I-BY151 Link to I-BY151 on YFull View heatmap on Y Heatmap View theoretical migration on PhyloGeographer

I-BY151 BY151+
┣━I-BY351 +3 BY351- BY352-
┣━I-BY62 +2 A29275- BY62- Y182584-
┣━I-FGC81364 +2 FGC81364- FGC9508(?)
┗━I-S11545 +1 FT30947- S11545- S15291- S15818- S19233- S19965- S25537- Y19875- Y19876- Y19878- Y19882- Y33202-

Negative for all known downstream SNPs

Available Panels
YSEQ recommends the I1-Z63 Panel Predicted I-BY151 is downstream of the panel root. This panel may be applicable if it tests subclades below I-BY151. Please verify and check with YSEQ customer support.


A bit confusing as it does seem to contradict the 23andme results. I guess they're uploading the results and I'll receive more info in the next few days, as I can't really understand much right now.

MacUalraig
12-02-2021, 09:57 PM
I have not received an email with the results but I've just logged in the website and on "My Allele Results" I've got this:

Most specific position on the YFull YTree is I-BY151 Link to I-BY151 on YFull View heatmap on Y Heatmap View theoretical migration on PhyloGeographer

I-BY151 BY151+
┣━I-BY351 +3 BY351- BY352-
┣━I-BY62 +2 A29275- BY62- Y182584-
┣━I-FGC81364 +2 FGC81364- FGC9508(?)
┗━I-S11545 +1 FT30947- S11545- S15291- S15818- S19233- S19965- S25537- Y19875- Y19876- Y19878- Y19882- Y33202-

Negative for all known downstream SNPs

Available Panels
YSEQ recommends the I1-Z63 Panel Predicted I-BY151 is downstream of the panel root. This panel may be applicable if it tests subclades below I-BY151. Please verify and check with YSEQ customer support.


A bit confusing as it does seem to contradict the 23andme results. I guess they're uploading the results and I'll receive more info in the next few days, as I can't really understand much right now.

To be honest I hadn't looked under that section for kits doing WGS. It's more of a haplogroup summary and I agree a bit confusing (especially the implication you need to do a panel test). If its off the WGS it should either match or have finer resolution than your 23andMe test though. Did the other test put you in a sibling branch? Or just higher up/lower down the one you mention?

Northern Adriatic
12-02-2021, 10:06 PM
To be honest I hadn't looked under that section for kits doing WGS. It's more of a haplogroup summary and I agree a bit confusing (especially the implication you need to do a panel test). If its off the WGS it should either match or have finer resolution than your 23andMe test though. Did the other test put you in a sibling branch? Or just higher up/lower down the one you mention?
Thanks for replying :)

The 23andme test gave me as a result I-Z58, negative for I-Z59 and I-Z138. YSEQ is giving me I-Z63, so an entire different result (although both I1a).

To be fair I have checked the website because after asking for an update on my results just yesterday they told me that the results were due in a few days. I have not yet received an email and browsing around the YSEQ website it seems to be that a lot of the results need to be uploaded yet, so this may be provisional, maybe :\

MacUalraig
12-02-2021, 10:19 PM
Thanks for replying :)

The 23andme test gave me as a result I-Z58, negative for I-Z59 and I-Z138. YSEQ is giving me I-Z63, so an entire different result (although both I1a).

To be fair I have checked the website because after asking for an update on my results just yesterday they told me that the results were due in a few days. I have not yet received an email and browsing around the YSEQ website it seems to be that a lot of the results need to be uploaded yet, so this may be provisional, maybe :\

Ok so we are talking two sibling branches then. You should have your raw data (BAM file) shortly then you can check it all manually if necessary including the Z58 status. I do know a batch just completed in the last few days as I had the two kits from it I was waiting for.

Northern Adriatic
12-03-2021, 06:52 PM
I have received my results. The webpage of YSEQ does not seem to be fully updated yet (for example in My STR Results), but in the email is confirmed the following (unexpected) path: A0-T > A1 > A1b > BT > CT > CF > F > GHIJK > HIJK > IJK > IJ > I > I1 > I-L121 > I-DF29 > I-Z63 > I-BY151.

I will upload to Y-Full to double check I guess.

For the genome, does anybody know which file should be sent to Davidski for the G25 Coordinates?

MacUalraig
12-03-2021, 08:56 PM
I have received my results. The webpage of YSEQ does not seem to be fully updated yet (for example in My STR Results), but in the email is confirmed the following (unexpected) path: A0-T > A1 > A1b > BT > CT > CF > F > GHIJK > HIJK > IJK > IJ > I > I1 > I-L121 > I-DF29 > I-Z63 > I-BY151.

I will upload to Y-Full to double check I guess.

For the genome, does anybody know which file should be sent to Davidski for the G25 Coordinates?

I don't do G25 work but the equivalent of an autosomal chip test is the '23andMe' file which should be zipped up in the results folder. Its a composite of the SNPs from Ancestry, 23andMe etc so has something like 1.5M rows but its formatted as if it were a 23andMe test. Filename will be something like:

99999_23andMe_all_hg19.zip

where 99999 is your kitnumber. It's the only file in hg19 mapping, the rest should be hg38.

Northern Adriatic
12-03-2021, 11:59 PM
Thx MacUalraig!

BTW, just uploading the y-dna bam and bam.bai to https://qual.iobio.io/

Item Value Expected
Read Length 390.87 Should be almost exactly 100, 150, etc
Raw GBases 0.29 >90; less than 90 and Dante will re-sequence
% Mapped 100.00 Looking for 95% or higher
Mapped Avg Read Depth 0.09 Preferably >30 (the real source of the 30x declaration)

Chr/DNA Len in model (bp) # Mapped # Unmapped Mapped GBases Avg Read Depth
chrY 57227415 734795 0 0.29 5x

JamesKane
12-06-2021, 03:44 AM
The qual.iobio.io site is based around the assumption you are testing with traditional run settings and 30x coverage.

The WGS400 product currently offered is 15x with 400 base SE reads, so basically everything it's claiming about expectations are wrong.

5x chrY is pretty low but within the range I'm seeing for those added into https://ydna-warehouse.org/benchmarks.

jadegreg
12-06-2021, 12:55 PM
...........
For the genome, does anybody know which file should be sent to Davidski for the G25 Coordinates?

Best thing to do for that is to download a copy of WGSExtract, latest version, to pullout the relevant SNP dataset for his analysis

https://wgsextract.github.io/

You're best bet is to probably do is send him the 23&me v3 extract of your WGS data, or a combined 23&me (v3-v5) dataset for your G25 coordinates

capsian
12-06-2021, 03:16 PM
Thx MacUalraig!

BTW, just uploading the y-dna bam and bam.bai to https://qual.iobio.io/

Item Value Expected
Read Length 390.87 Should be almost exactly 100, 150, etc
Raw GBases 0.29 >90; less than 90 and Dante will re-sequence
% Mapped 100.00 Looking for 95% or higher
Mapped Avg Read Depth 0.09 Preferably >30 (the real source of the 30x declaration)

Chr/DNA Len in model (bp) # Mapped # Unmapped Mapped GBases Avg Read Depth
chrY 57227415 734795 0 0.29 5x

Hi it seems to me this sample it your YF94852^
i have been see you have 3X this it's bad

capsian
12-06-2021, 03:21 PM
The qual.iobio.io site is based around the assumption you are testing with traditional run settings and 30x coverage.

The WGS400 product currently offered is 15x with 400 base SE reads, so basically everything it's claiming about expectations are wrong.

5x chrY is pretty low but within the range I'm seeing for those added into https://ydna-warehouse.org/benchmarks.

do you can explain more and thanks

Biharguy
12-06-2021, 04:59 PM
Some stats from Yfull on samples I uploaded.

47678

The WGS400 underperforms quite a bit from the stated 15x depth coverage.

JamesKane
12-06-2021, 05:10 PM
do you can explain more and thanks

The online tool that you used is built around the assumption you have ordered a 30x WGS test run on Illumina sequencers. It's the "standard" that most sequencing has been performed with to date. The textual guidance is biased towards those assumptions.

With a 30x test you need to read roughly 3 billion locations 30 times and wind up with the raw 90 GBases the report references.

The average depth comes from sampling each chromosome about 15x. As a male you have two slightly different copies of each chromosome except X and Y. That's why you only see 15x coverage on the Y chromosome.

Now as to why it's not entirely relevant with WGS400.

1) It's only a 15x test in its current incarnation. Therefore about 45 GBases are delivered.
2) The fast method used to generate the coverage depth on the Y chromosome is flat wrong. It's including the N base locations in the reference, which reads cannot be assigned to anyway. You can only count depth where the alignment can occur in the first place.
3) Similarly, the fast method gets the read length estimates wrong. I haven't seen any of these that is not 400, which is not a run mode available on Illumina sequencers.

In conversation with Thomas, they do plan to offer deeper coverage in the future but are keeping the 15x as the standard target.

JamesKane
12-06-2021, 05:16 PM
Some stats from Yfull on samples I uploaded.

47678

The WGS400 underperforms quite a bit from the stated 15x depth coverage.

7 to 8x is the expected level of coverage for the Y chromosome in a 15x WGS test.

15x is a 30x test.

30x is a 60x test.

etc...

The only thing I would expect lower coverage to impact is the ability to call STRs. You simply need more of them to bridge the length of the feature even though you have 2.67x longer reads.

capsian
12-06-2021, 07:27 PM
The online tool that you used is built around the assumption you have ordered a 30x WGS test run on Illumina sequencers. It's the "standard" that most sequencing has been performed with to date. The textual guidance is biased towards those assumptions.

With a 30x test you need to read roughly 3 billion locations 30 times and wind up with the raw 90 GBases the report references.

The average depth comes from sampling each chromosome about 15x. As a male you have two slightly different copies of each chromosome except X and Y. That's why you only see 15x coverage on the Y chromosome.

Now as to why it's not entirely relevant with WGS400.

1) It's only a 15x test in its current incarnation. Therefore about 45 GBases are delivered.
2) The fast method used to generate the coverage depth on the Y chromosome is flat wrong. It's including the N base locations in the reference, which reads cannot be assigned to anyway. You can only count depth where the alignment can occur in the first place.
3) Similarly, the fast method gets the read length estimates wrong. I haven't seen any of these that is not 400, which is not a run mode available on Illumina sequencers.

In conversation with Thomas, they do plan to offer deeper coverage in the future but are keeping the 15x as the standard target.

thank for informations

capsian
12-06-2021, 07:49 PM
The online tool that you used is built around the assumption you have ordered a 30x WGS test run on Illumina sequencers. It's the "standard" that most sequencing has been performed with to date. The textual guidance is biased towards those assumptions.

With a 30x test you need to read roughly 3 billion locations 30 times and wind up with the raw 90 GBases the report references.

The average depth comes from sampling each chromosome about 15x. As a male you have two slightly different copies of each chromosome except X and Y. That's why you only see 15x coverage on the Y chromosome.

Now as to why it's not entirely relevant with WGS400.

1) It's only a 15x test in its current incarnation. Therefore about 45 GBases are delivered.
2) The fast method used to generate the coverage depth on the Y chromosome is flat wrong. It's including the N base locations in the reference, which reads cannot be assigned to anyway. You can only count depth where the alignment can occur in the first place.
3) Similarly, the fast method gets the read length estimates wrong. I haven't seen any of these that is not 400, which is not a run mode available on Illumina sequencers.

In conversation with Thomas, they do plan to offer deeper coverage in the future but are keeping the 15x as the standard target.
what do you think it seems to me it s good
4767947680

JamesKane
12-06-2021, 07:57 PM
what do you think it seems to me it s good
4767947680

The screenshots show that it's over-performing. The results are closer to a 20x test but this is only the Y chromosome. You need the hg38_sorted.bam to know the overall quality of the test. The Y chromosome is a tiny fraction of what you bought with these tests.

capsian
12-06-2021, 08:06 PM
The screenshots show that it's over-performing. The results are closer to a 20x test but this is only the Y chromosome. You need the hg38_sorted.bam to know the overall quality of the test. The Y chromosome is a tiny fraction of what you bought with these tests.
thanks
where i can find hg38_sorted.bam

JamesKane
12-06-2021, 08:25 PM
It should be on the genomes server in the folder you were given access to. The name pattern looks like this:
[kit#]_bwa-mem_hg38_sorted.bam

It's quite possible you need to contact [email protected] to copy the full BAM in these days. I see mine isn't visible anymore, but it could also be I'm logged in via ydna-warehouse's service account which can't see them for privacy reasons.

Northern Adriatic
12-06-2021, 11:13 PM
Hi it seems to me this sample it your YF94852^
i have been see you have 3X this it's bad
Indeed.

90.92% Length coverage
3X Median depth coverage
745X MAX
5.18X MEAN
1X MIN

capsian
12-07-2021, 01:08 PM
Indeed.

90.92% Length coverage
3X Median depth coverage
745X MAX
5.18X MEAN
1X MIN

do you think it s good or no

MacUalraig
12-07-2021, 04:35 PM
It should be on the genomes server in the folder you were given access to. The name pattern looks like this:
[kit#]_bwa-mem_hg38_sorted.bam

It's quite possible you need to contact [email protected] to copy the full BAM in these days. I see mine isn't visible anymore, but it could also be I'm logged in via ydna-warehouse's service account which can't see them for privacy reasons.

They stopped uploading the WGS BAMs as default some time ago, they upload the chrY BAM and put a notice up to put you off the other one:

"Please let us know if you want us to upload your complete WGS BAM file to our webserver.
The upload will take several days.
The complete BAM file of your genome will be available here:
https://genomes.yseq.net/WGS/???_bwa-mem_hg38_sorted.bam
https://genomes.yseq.net/WGS/???_bwa-mem_hg38_sorted.bam.bai (index file)
Please be aware that this is a huge download of 30 Gbyte.
"

Robert McBride
12-19-2021, 07:48 PM
47801

My WGS400 15x was ordered 16 Feb and delivered September 14th. I ordered YFull the next day but the YFULL STR verification was only finished last Friday.

The first column is my original Big Y, the second Yseq WGS150 50x, the third Big Y700 and the fourth WGS400 15x .

peloponnesian
02-03-2022, 03:02 PM
Here's a waiting time (weeks) histogram that T. Krahn of YSEQ has collected for the last WGS400 batch as of October 18th:

https://i.gyazo.com/2f6c3b599c314481c41e9dc45b2a6c6e.jpg

I'm close to 6 months waiting at the moment. Clearly they have a big workload but their process seems kind of random and arbitrary. I get the impression that with some of these smaller DNA companies you have to pester them every day with emails and threats in order to get your results in a timely manner which seems like a bad business practice.

Northern Adriatic
02-03-2022, 03:34 PM
I'm close to 6 months waiting at the moment. Clearly they have a big workload but their process seems kind of random and arbitrary. I get the impression that with some of these smaller DNA companies you have to pester them every day with emails and threats in order to get your results in a timely manner which seems like a bad business practice.
I had the same impression.

Seeing that many people had different waiting times to get their results, after ordering the test in mid-August and sending my samples back before the end of the month, I wrote them in early October to ask for updates. Once I have received the same graph posted in this thread I wrote them again in late november without receiving any reply.

I wrote them again in the first days of December making reference to the waiting times and asking if they had to do a re-run or the results were going to be sent in the next few days. At that point they told me that results were due by the end of the week and a few days later I got my results.

peloponnesian
02-03-2022, 03:51 PM
I had the same impression.

Seeing that many people had different waiting times to get their results, after ordering the test in mid-August and sending my samples back before the end of the month, I wrote them in early October to ask for updates. Once I have received the same graph posted in this thread I wrote them again in late november without receiving any reply.

I wrote them again in the first days of December making reference to the waiting times and asking if they had to do a re-run or the results were going to be sent in the next few days. At that point they told me that results were due by the end of the week and a few days later I got my results.

Doesn't sound like you bothered them too much, judging by their FB page they have some angry customers right now :P

If there was a problem with my sample I expect they'd have at least mentioned it so I doubt they had to do a re-run.

teepean47
02-03-2022, 05:07 PM
I had the same impression.

Seeing that many people had different waiting times to get their results, after ordering the test in mid-August and sending my samples back before the end of the month, I wrote them in early October to ask for updates. Once I have received the same graph posted in this thread I wrote them again in late november without receiving any reply.

I wrote them again in the first days of December making reference to the waiting times and asking if they had to do a re-run or the results were going to be sent in the next few days. At that point they told me that results were due by the end of the week and a few days later I got my results.

It happened with Dante and Nebula: offer a cheap WGS + get huge amount of orders and be unprepared = a lot of angry customers waiting for their results.

MacUalraig
02-04-2022, 05:56 PM
It happened with Dante and Nebula: offer a cheap WGS + get huge amount of orders and be unprepared = a lot of angry customers waiting for their results.

Hard to compare without the full data, and those two initially were outsourcing before Dante went in-house. YSEQ's outsourced service was extremely fast (typically ~5 weeks) and their WGS400 started off ok from what I can make out. It isn't clear if everyone is delayed or not, I've had turnarounds ranging from 2 months to forever.

peloponnesian
02-04-2022, 06:44 PM
I got some preliminary results yesterday, they'll have to do another sequencing run but the quality is expected to be good. I'll post the stats once I have the full results. To be clear, Thomas and Astrid have been very helpful whenever I asked them a technical question and I'm sure they've been working very hard to keep up with their backlog.

ChrisR
02-05-2022, 08:51 PM
https://ydna-warehouse.org/benchmarks shows 50x, 20x and 15x for WGS400: I asked Astrid what is currently the depth/resolution for 399€ (see website (https://www.yseq.net/product_info.php?cPath=29&products_id=175886)) and what other depths can be ordered. If anyone here knows thanks for sharing.

It seems for men/Y the depth should be 20x or better 30x, while 50x seems to bring little additional benefit.
The other observation (based on only a few kits) seems to be that WGS150 or WGS400 is not much different for Est. Years/SNP when looking at 15x, 20x and 50x

peloponnesian
04-07-2022, 12:24 PM
I got my results for the WGS 400 test, I'm waiting for Yfull to finish their analysis so I can post the stats for the Y chromosome.

peloponnesian
04-07-2022, 08:34 PM
I got these stats from Yfull:

ChrY BAM file size: 0.20 GbHg38
Reads (all): 621131
Read length: 400 bp
Mapped reads: 621131(100.00%)
Unmapped reads: 0
Length coverage: 23095148 bp(97.71%)
Min depth coverage: 1X
Max depth coverage: 737X
Mean depth coverage: 6.44X
Median depth coverage: 5X
Length coverage for age*: 6997178 bp
No call: 541207 bp

SNPs (all): 288386
Positive: 2807 (0.97%)
Negative: 14562 (5.05%)
Ambiguous: 139 (0.05%)
No call: 369 (0.13%)

STRs (all): 780
Reliable alleles: 263 (33.72%)
Uncertain alleles: 340 (43.59%)
N/A: 177 (22.69%)

Novel SNPs (all): 87
Best qual: 69 (79.31%) [52 (59.77%) - best; 17 (19.54%) - acceptable]
INDELs: 0
Ambiguous qual: 2 (2.30%)
One read!: 13 (14.94%)
Low qual: 3 (3.45%)

Still not able to access the specific SNP pages etc because there's a holdup with Yfull payment.

JMcB
04-07-2022, 11:47 PM
I got these stats from Yfull:

ChrY BAM file size: 0.20 GbHg38
Reads (all): 621131
Read length: 400 bp
Mapped reads: 621131(100.00%)
Unmapped reads: 0
Length coverage: 23095148 bp(97.71%)
Min depth coverage: 1X
Max depth coverage: 737X
Mean depth coverage: 6.44X
Median depth coverage: 5X
Length coverage for age*: 6997178 bp
No call: 541207 bp

SNPs (all): 288386
Positive: 2807 (0.97%)
Negative: 14562 (5.05%)
Ambiguous: 139 (0.05%)
No call: 369 (0.13%)

STRs (all): 780
Reliable alleles: 263 (33.72%)
Uncertain alleles: 340 (43.59%)
N/A: 177 (22.69%)

Novel SNPs (all): 87
Best qual: 69 (79.31%) [52 (59.77%) - best; 17 (19.54%) - acceptable]
INDELs: 0
Ambiguous qual: 2 (2.30%)
One read!: 13 (14.94%)
Low qual: 3 (3.45%)

Still not able to access the specific SNP pages etc because there's a holdup with Yfull payment.


For your possible interest, in case you haven’t already seen it. This was posted on their Facebook page yesterday.

Dear customers! We have the opportunity to accept payment from you using PayPal. Currently, there is only the PayPal method so far and we accept payments from only old orders (up to the number YF101000 inclusive). We will gradually open this opportunity to everyone. As payments are processed, we will send notifications to the owners of samples with numbers greater than YF101000. We are working to establish to pay by cards as before. We hope for your understanding.

peloponnesian
04-08-2022, 02:12 PM
For your possible interest, in case you haven’t already seen it. This was posted on their Facebook page yesterday.

Dear customers! We have the opportunity to accept payment from you using PayPal. Currently, there is only the PayPal method so far and we accept payments from only old orders (up to the number YF101000 inclusive). We will gradually open this opportunity to everyone. As payments are processed, we will send notifications to the owners of samples with numbers greater than YF101000. We are working to establish to pay by cards as before. We hope for your understanding.

Thanks, today I tried again and it worked. Their PayPal account is based outside of Russia so there shouldn't be any problems with that method.

BTW, both me and NorthernAdriatic got very bad statistics for our STR results. Lots of values missing, basically unusable. They should clarify it to their customers IMO because their website advertises STR results as a benefit of the WGS400.

MacUalraig
04-08-2022, 04:38 PM
Thanks, today I tried again and it worked. Their PayPal account is based outside of Russia so there shouldn't be any problems with that method.

BTW, both me and NorthernAdriatic got very bad statistics for our STR results. Lots of values missing, basically unusable. They should clarify it to their customers IMO because their website advertises STR results as a benefit of the WGS400.

But presumably they haven't actually done the STR results formally yet? That usually comes along some time after you pay for the SNP analysis. I can't remember if the numbers change much. I got my WGS400 recently but not sent it to YFull yet. Certainly I got much better STRs from my previous YSEQ 30x but you've got a sub-par 15x there (6x chrY).

MacUalraig
04-08-2022, 04:40 PM
For your possible interest, in case you haven’t already seen it. This was posted on their Facebook page yesterday.

Dear customers! We have the opportunity to accept payment from you using PayPal. Currently, there is only the PayPal method so far and we accept payments from only old orders (up to the number YF101000 inclusive). We will gradually open this opportunity to everyone. As payments are processed, we will send notifications to the owners of samples with numbers greater than YF101000. We are working to establish to pay by cards as before. We hope for your understanding.

I don't/can't use PayPal so I will await their further news ..

Northern Adriatic
04-08-2022, 04:50 PM
But presumably they haven't actually done the STR results formally yet? That usually comes along some time after you pay for the SNP analysis. I can't remember if the numbers change much. I got my WGS400 recently but not sent it to YFull yet. Certainly I got much better STRs from my previous YSEQ 30x but you've got a sub-par 15x there (6x chrY).
A few months later in my case and the result was:
Reliable Alleles: 43.2%
Uncertain: 20.4%
N/A Alleles: 36.4%

peloponnesian
04-09-2022, 02:03 PM
But presumably they haven't actually done the STR results formally yet? That usually comes along some time after you pay for the SNP analysis. I can't remember if the numbers change much. I got my WGS400 recently but not sent it to YFull yet. Certainly I got much better STRs from my previous YSEQ 30x but you've got a sub-par 15x there (6x chrY).

How do you mean? Yfull sent me an email saying "Your STR data analysis has been successfully completed"


I got my WGS400 recently but not sent it to YFull yet. Certainly I got much better STRs from my previous YSEQ 30x but you've got a sub-par 15x there (6x chrY).

Well, that's not the impression one gets after reading this: https://www.yseq.net/product_info.php?products_id=175886. They don't mention the possibility of missing half the STR markers.

And the result being subpar (5x rather than 7-8x) isn't my fault, they never asked me if I want to send in a new sample.

MacUalraig
04-09-2022, 03:11 PM
In normal times they do the SNP analysis, bill you then after you pay they do the STR analysis which follows sometimes at a very long time interval. It goes without saying that these are not normal times.

The STRs are of little use and don't bother me personally. Missed SNPs would bother me a lot but your chrY coverage is probably OK to not worry too much about that. I've had kits with similar coverage results and been content with them. What is needed is to get onto the YFull SNP tree and have good SNP matching. The STR matching they offer is just a toy since it still has an element of false positive matching when checked against the SNP tree, which is why I ignore them.

MacUalraig
04-14-2022, 06:20 PM
It seems YSEQ have introduced/re-introduced the 15-50x WGS but with the 150bp PE reads not at 400bp. This is intriguing because at one stage I requested to run a kit via the 'old' outsourced 15x and they declined the order (although the two principals advanced different excuses why they couldn't do it...). The 400bp is still on but note:

"Thomas Krahn
Admin
All currently outstanding WGS400 samples will be processed as WGS+, unless somebody specifically asks us for 400 base reads. That means a minimum of 90 GBases."

randalgibbs
04-15-2022, 12:52 AM
The website now shows 4 tests for sale.

https://www.yseq.net/index.php?cPath=29

WGS $359 150bp 15x (was $599)
WGS+ $399 150bp 30x (was $949)
WGS++ $699 150bp 50x (was $1599)
WGS400 $399 400bp 15x

The pricing is odd. Why pay $359 for 15x, if you can get 30x for another $40?

MacUalraig
04-15-2022, 08:42 AM
The website now shows 4 tests for sale.

https://www.yseq.net/index.php?cPath=29

WGS $359 150bp 15x (was $599)
WGS+ $399 150bp 30x (was $949)
WGS++ $699 150bp 50x (was $1599)
WGS400 $399 400bp 15x

The pricing is odd. Why pay $359 for 15x, if you can get 30x for another $40?

Well, he knows his rivals (Nebula and Sequencing.com) have established 30x as the entry standard so clearly he wants people to go for that.

teepean47
04-15-2022, 04:07 PM
The website now shows 4 tests for sale.

https://www.yseq.net/index.php?cPath=29

WGS $359 150bp 15x (was $599)
WGS+ $399 150bp 30x (was $949)
WGS++ $699 150bp 50x (was $1599)
WGS400 $399 400bp 15x

The pricing is odd. Why pay $359 for 15x, if you can get 30x for another $40?

400bp 30x or 50x would have been a nice addition.

Fitis
04-16-2022, 01:38 PM
I am happy with my results of WGS from YSEQ (Mean depth coverage: 23.18X) this week.
I ordered a WGS400 (399$) but I finally got a WGS with 150bp (I have 45X on the autosomes so 30X or 50X?).
Here is a comparison with my BIG-Y from FTDNA:

https://zupimages.net/up/22/15/622u.png (https://zupimages.net/viewer.php?id=22/15/622u.png)

ChrisR
04-19-2022, 08:03 PM
For a male without sequencing I was interested in WGS400 400bp 30x (YSEQ in 2021 said it would run two times the 15x if so ordered) but it seems that WGS+ 150bp 30x or WGS++ 150bp 50x are the better "entry" tests when focusing on the Y
WGS400 seems like an additional test (for the Y) but the complexity of data merging (or using of two results) remains a question for me.

EDIT: ordered two WGS+ 30x and one WGS++ 50x. For now no WGS400. According to Astrid sequencing is still mostly done with their own sequencer in an external lab, but it is planned to bring the machine to their main lab this year, so they will do all the work inhouse. Looking forward to the results.

MacUalraig
05-17-2022, 05:10 PM
I've got a couple of conversions from WGS400 to WGS+ pending but not ordered one as new until I see the conversions. Please report delivery timelines if you order new.

sirdan
05-18-2022, 06:17 AM
WGS400 is a product for better STR detection. Problem is that often STR markers differ between companies like from FTDNA vs others. Single STR markers do not match from the same person. I would be afraid to compare them and make assumptions. One way to omit this is to test all family members in one company.

Also When having good depth coverage in WGS and low "no calls" count is good enough for high quality test.

Anyway, high depth coverage and long base reads are the future of WGS.

MacUalraig
05-18-2022, 06:34 AM
WGS400 is a product for better STR detection.

According to YSEQ Marketing Department. I never thought that was a good selling point myself. If it gives better or more SNPs, or some further stable variants we haven't used before, that is good. Unfortunately my own sample didn't turn out that well so the jury is still out from my POV.

G-Man
06-01-2022, 02:35 PM
YFull stats of my friend's WGS400:

https://i.ibb.co/kHCr0Gk/YSEQ-1.png

https://i.ibb.co/SwVkHy0/YSEQ-2.png

Everything is very bad. Sample not included in TMRCA calculations.


https://i.ibb.co/DpnGh3R/YSEQ-3.png

Better STR detection?


And this is not an isolated case. You can see many of these bad WGS400 samples on the YFull tree.

Adamm
06-01-2022, 03:18 PM
YFull stats of my friend's WGS400:

https://i.ibb.co/kHCr0Gk/YSEQ-1.png

https://i.ibb.co/SwVkHy0/YSEQ-2.png

Everything is very bad. Sample not included in TMRCA calculations.


https://i.ibb.co/DpnGh3R/YSEQ-3.png

Better STR detection?


And this is not an isolated case. You can see many of these bad WGS400 samples on the YFull tree.

How much did you paid for that? I thought my raw data was bad (11x on median depth).

Gentica277282
06-01-2022, 03:28 PM
How much did you paid for that? I thought my raw data was bad (11x on median depth).

Mine is 15x what’s it meant to be

G-Man
06-01-2022, 03:40 PM
How much did you paid for that? I thought my raw data was bad (11x on median depth).

$399.00

Yeah, I was a bit shocked when I saw these stats :)

Didn't expect this from YSEQ

Adamm
06-01-2022, 06:32 PM
Mine is 15x what’s it meant to be

Basically how more reads how better, I think for reliable results the reads on your Y-DNA needs to be at least a certain number which I forgot.

Adamm
06-01-2022, 06:32 PM
$399.00

Yeah, I was a bit shocked when I saw these stats :)

Didn't expect this from YSEQ

Should've gone with Nebula or Dante, majority of their results are good enough for YFULL.

MacUalraig
06-01-2022, 07:55 PM
Mine is 15x what’s it meant to be

Their short read WGS are advertised at 15x/30x/50x on the product description. The WGS400 product description never stated the depth, I think it was 'understood' to be 15x but it didn't work out that way for a lot of folk. The sample data for the WGS400 was actually a 50x.

capsian
06-12-2022, 05:37 PM
YFull stats of my friend's WGS400:

https://i.ibb.co/kHCr0Gk/YSEQ-1.png

https://i.ibb.co/SwVkHy0/YSEQ-2.png

Everything is very bad. Sample not included in TMRCA calculations.


https://i.ibb.co/DpnGh3R/YSEQ-3.png

Better STR detection?


And this is not an isolated case. You can see many of these bad WGS400 samples on the YFull tree.

ChrY BAM file size: 0.33 GbHg38
Reads (all): 1049461
Read length: 400 bp
Mapped reads: 1049461(100.00%)
Unmapped reads: 0
Length coverage: 23425373 bp(99.11%)
Min depth coverage: 1X
Max depth coverage: 752X
Mean depth coverage: 11.02X
Median depth coverage: 9X
Length coverage for age*: 8151079 bp
No call: 210982 bp


SNPs (all): 299424
Positive: 3023 (1.01%)
Negative: 16139 (5.39%)
Ambiguous: 77 (0.03%)
No call: 153 (0.05%)



STRs (all): 780
Reliable alleles: 498 (63.85%)
Uncertain alleles: 124 (15.90%)
N/A: 158 (20.26%)


Novel SNPs (all): 20
Best qual: 11 (55.00%) [9 (45.00%) - best; 2 (10.00%) - acceptable]
INDELs: 0
Ambiguous qual: 1 (5.00%)
One read!: 7 (35.00%)
Low qual: 1 (5.00%)