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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