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Searcher
12-09-2017, 02:15 AM
I got my autosomal testing done at 23andme and I want to find out my SNPs and real mtDNA. Is this the way to go? It seems cheaper but it might be missing important things.

JamesKane
12-09-2017, 03:36 AM
Ultimately, the decision depends on what you wish to learn, how much personal investment of time you wish to make, and the closest haplogroup project that your 23&Me test turned up.

The cost for mtDNA at YSEQ is attractive but most of the mtDNA projects live within FTDNA's ecosystem. You can share the results with those admins or run them through James Lick's https://dna.jameslick.com/mthap/ to find your terminal group. The downside is you can't participate in matching. The usefulness of mtDNA matches is debatable though.

When it comes to the Y panels, I really like the R1b versions of YSEQ's products. In many cases they are more comprehensive than the FTDNA equivalent, since they can be updated on the fly when group admins report new branches to the YSEQ team. With FTDNA you are still locked into their STR testing system with Y DNA. All of their matching systems are predicated on having STR results. Depending on your SNP branch these may be unnecessary, since NGS testing has been turning up genealogically relevant branches. Outside of R this might not be the case though.

MacUalraig
12-09-2017, 07:56 AM
I would broadly agree with what James says. mtDNA is little more than a curiosity. For Y SNPs YSEQ are very good and 'matching' can be done on forums, fb, google etc. FTDNA don't do SNP matching - they just display what SNPs are available (if any) for whoever pops up in your STR match list, and the correlation between SNP and STR matches can be poor.

Searcher
01-18-2018, 06:18 PM
Thank you all for the assistance.

Just a quick question. If my 23andme autosomal Y-Hap guess was H-M52, what do I purchase from Yseq?

gotten
01-18-2018, 07:38 PM
The H-L901 panel contains M52 and its subclades: https://www.yseq.net/product_info.php?cPath=27&products_id=56678

Searcher
01-19-2018, 02:17 AM
Thanks!

karwiso
01-19-2018, 02:35 AM
My opinion is:

1. mtDN - FamilyTreeDNA. Very good quality (better than Whole Genome Sequencing) and the size of the database.

2. Transfer your 23andme results to FTDNA. No, I wouldn't do it. FTDNA has a chip tha is a lot different. Just order FamilyFinder with the next sale.

3. If it is Y chromosome, than I would do Y-67 or Y-111, I don't find BigY so wonderful and I would recommend to do WGS and YFull.

Marmaduke
01-19-2018, 03:19 AM
Which company do you recommend for WGS, and why?

JamesKane
01-19-2018, 10:51 AM
I ordered mine from YSEQ when they announced their lab partner is using the current generation NovaSEQ instruments. This was a more expensive option than going with the current price leader in the segment, Dante Labs. The reasoning for going this route is Dante is very tight lipped about the statistics of the test being performed and the read lengths match those in my old Y Elite test. The YSEQ offering is the bigger upgrade as far what was available and what I was willing to spend.

That said I should have metrics for the Dante Labs results coverage in the next few days and will be able to add them to the Y DNA NGS coverage comparison.

morrisondna
01-19-2018, 04:33 PM
I ordered mine from YSEQ when they announced their lab partner is using the current generation NovaSEQ instruments. This was a more expensive option than going with the current price leader in the segment, Dante Labs. The reasoning for going this route is Dante is very tight lipped about the statistics of the test being performed and the read lengths match those in my old Y Elite test. The YSEQ offering is the bigger upgrade as far what was available and what I was willing to spend.

That said I should have metrics for the Dante Labs results coverage in the next few days and will be able to add them to the Y DNA NGS coverage comparison.

I have also ordered WGS from YSEQ --- two tests so far. Turnaround time was excellent and service outstanding.

karwiso
01-19-2018, 07:46 PM
Which company do you recommend for WGS, and why?

I have ordered 6 WGS from Dante Labs. During the sales and Black Friday there were very good offers so I could afford to order several tests. I thought it was a better option than paying more just for 1 or 2 WGS. Yes, the read length is 100bp, not 150bp or 250bp as in other tests, but the coverage is 30x so it is still quite good. I think it is not so important with those differences in read length, we should expect more progress when long read WGS (kbp or mbp) will be available. The turn around time at Dante Labs is 10 weeks, you have to request BAM-files, but at no charge. One drawback - they align to GRCh37, not GRCh38 that is almost standard everywhere now.

Jan_Noack
01-25-2018, 06:18 AM
I ordered mine from YSEQ when they announced their lab partner is using the current generation NovaSEQ instruments. This was a more expensive option than going with the current price leader in the segment, Dante Labs. The reasoning for going this route is Dante is very tight lipped about the statistics of the test being performed and the read lengths match those in my old Y Elite test. The YSEQ offering is the bigger upgrade as far what was available and what I was willing to spend.

That said I should have metrics for the Dante Labs results coverage in the next few days and will be able to add them to the Y DNA NGS coverage comparison.
Hi James,
I'd be interested in your results and in the read length of Dante and YSEQ WGS tests.
Also, I guess I'm a relative newbie here and hoping you may be able to help. I like the YSEQ WGS test. I am considering the 15X but in previous WGS test at 15X there is reportedly not enough coverage to make as many calls as expected. It doesn't appear at all even coverage as I would expect. The 30X seem to overcome this but the BAM files or other type of data result files seem to be too big for other systems to handle..like promethease, GEDCOM? I guess a 20X for about the same relative price (ie 15X $740, 30X into $1190, so 20X (one third way between may hit about $890?) would be ideal! Of course it doesn't exist at YSEQ aat least as yet. Just wondering which you ordered , the 15X or the 30X and how you go about using the results elsewhere or even storing them online for uploading? Thanks

Marmaduke
01-25-2018, 06:44 AM
Full Genomes Corp. offers a 20x WGS for $820.

Jan_Noack
01-25-2018, 07:46 AM
Full Genomes Corp. offers a 20x WGS for $820.

here's post which made me choose the BigY instead of the 15X at the Xmas sales. It's by Petr last year

My FGC WGS 15x shows the statistic at YFull (Y chromosome):
Length coverage: 22547120 bp (87.89%)
Mean depth coverage: 13.08X
Median depth coverage: 6X

I don't have detail statistics, but it looks like this mean about 50 % coverage with depth 4 - 5 or better. For less than 4 reads there are too many error.

In comparison with typical Big Y

Length coverage: 14043329 bp (54.74%)
Mean depth coverage: 61.07X
Median depth coverage: 35X

It looks like the reliable coverage is almost the same.

It seems with new equipment and a different lab YSEQ have better stats fro their YSEQ at least on the one sample I saw quoted.
this may be not just due to better testing equipment, but also a longer read length? At the time I didn't realise YSEQ was doing WGS, I had thought they only did Sanger sequencing.

JamesKane
01-26-2018, 03:34 PM
Hi James,
I'd be interested in your results and in the read length of Dante and YSEQ WGS tests.

I went with the 30x option, since the primary driver for ordering the WGS is to get access to the autosomal data. 4 years later my Y Elite still holds up well as far as total amount of the Y chromosome sequenced. It's likely March before those results will come back.

For the Dante Y coverage stats see: https://anthrogenica.com/showthread.php?12075-Dante-Labs-(WGS)&p=338306&viewfull=1#post338306 Coverage lengths are on hg38, so this would be apples and pears for comparison with the FGC numbers in your post.

For YSEQs numbers...

50x WGS:
state nBases
REF_N 33591060
CALLABLE 15611634
NO_COVERAGE 36798
LOW_COVERAGE 155302
EXCESSIVE_COVERAGE 0
POOR_MAPPING_QUALITY 7869861

15x WGS:
state nBases
REF_N 33591060
CALLABLE 13299682
NO_COVERAGE 69491
LOW_COVERAGE 7234299
EXCESSIVE_COVERAGE 0
POOR_MAPPING_QUALITY 3070123

I don't have a 30x yet.

JamesKane
01-29-2018, 01:48 AM
I went with the 30x option, since the primary driver for ordering the WGS is to get access to the autosomal data. 4 years later my Y Elite still holds up well as far as total amount of the Y chromosome sequenced. It's likely March before those results will come back.

Just a quick correction on turn around time. Astrid posted my 30x WGS run on the NovaSEQ platform today. Total turn around was 30 days from when I dropped the sample off at the post office. Not too shabby since that includes about a week to get over the Atlantic to Berlin. Their analysis found everything named in my Y Elite except for FGC29057.

30x WGS (NovaSEQ):
state nBases
REF_N 33591060
CALLABLE 15303130
NO_COVERAGE 50935
LOW_COVERAGE 631600
EXCESSIVE_COVERAGE 0
POOR_MAPPING_QUALITY 7687930

morrisondna
01-30-2018, 11:29 PM
Just a quick correction on turn around time. Astrid posted my 30x WGS run on the NovaSEQ platform today. Total turn around was 30 days from when I dropped the sample off at the post office. Not too shabby since that includes about a week to get over the Atlantic to Berlin. Their analysis found everything named in my Y Elite except for FGC29057.


Great turnaround time considering we have an FGC Y Elite test still in process after 12 months. I ordered two 15X WGS tests from YSEQ and had results from both in under 12 weeks. Excellent service.

rock
02-01-2018, 02:22 PM
Great turnaround time considering we have an FGC Y Elite test still in process after 12 months. I ordered two 15X WGS tests from YSEQ and had results from both in under 12 weeks. Excellent service.

How about the Yfull Statistics of YSEQ 15x WGS?

morrisondna
02-01-2018, 05:24 PM
How about the Yfull Statistics of YSEQ 15x WGS?

No YFull data yet.

JamesKane
02-11-2018, 10:47 AM
Here's the YFULL data for one of YSEQ's new 30x WGS:

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

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

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

Ibericus
01-14-2020, 05:30 PM
Hi, I'm considering getting either Y-37 from FTDNA or the E superclade panel from Yseq. Which one would you choose? They are both in the $100 range.

JMcB
01-14-2020, 07:52 PM
It all depends on what you’re looking for. If you would like to get a more refined reading of where you are on the E haplotree, than I would go with YSEQ. If you’re more interested in seeing who your STR matches are, than I would go with Family Tree. What are you’re hoping to learn and if I may ask, how did you find out you were E1b1b?

Ayetooey
01-14-2020, 08:04 PM
Yseq can be better value than FTDNA when it comes to the straight up monetary cost, but I like the project aspect of FTDNA and the big Y test is pretty cool and informative if you ever wish to go down that route. There is really good discounts many times throughout the year, and they keep your spit file around so you can easily upgrade.

I don't know too much about Turnaround for YSEQ since I did everything at FTDNA, but my big Y results were predicted for February, I received them beginning of December, .

Ibericus
01-14-2020, 08:18 PM
It all depends on what you’re looking for. If you would like to get a more refined reading of where you are on the E haplotree, than I would go with YSEQ. If you’re more interested in seeing who your STR matches are, than I would go with Family Tree. What are you’re hoping to learn and if I may ask, how did you find out you were E1b1b?

I tested with Myheritage and then I used the Morley predictor, which assigned me E-M81.

I don't think I will get many matches so maybe I will go with Yseq and then I will do my own research once I have the results.

JMcB
01-14-2020, 08:38 PM
I tested with Myheritage and then I used the Morley predictor, which assigned me E-M81.

I don't think I will get many matches so maybe I will go with Yseq and then I will do my own research once I have the results.

Sounds like a reasonable plan. Good luck!

RobertCasey
01-14-2020, 08:56 PM
I would go with Y67, then use NEVGEN which predicts around 50 % of testers with high accuracy. With Y67 in hand, you can determine your matches and usually can predict 80 % of all testers via empirical YSNP prediction. You can also put your matches into an EXCEL spreadsheet, copy and paste into the SAPP input format which will produce a chart of how all your matches are related to each other. Haplogroup E is much less tested that Haplogroup R, so the above percentages may be somewhat lower. If you want to put minimal costs into testing but are willing to spend time, there is enough Big Y testing going on these days that many may not need any FGS or WGS test to find out how they are related to others. Y111 upgrade are good if a lot of your matches are at Y111. However, in five to ten years, Y500, Y700 and Y1500 YSTRs will reveal more than the YSNP testing will which is now reaching its limit of usefulness for 10 to 20 % of all YDNA testers (it probably has more mileage under Haplogroup E which is less tested to date).

Ruderico
01-14-2020, 09:47 PM
If you decide for FTDNA make sure you join the E-M35 project, I'm there myself and find it quite good

aaronbee2010
01-15-2020, 09:02 PM
I got my autosomal testing done at 23andme and I want to find out my SNPs and real mtDNA. Is this the way to go? It seems cheaper but it might be missing important things.

For Y-DNA and mtDNA together, you would be best off with Dante Labs x30 WGS on offer ($170 with multiple discounts on the last Black Friday and free shipping), as you get Y-DNA and mtDNA sequencing data, as well as the ability to generated enhanced autosomal data with WGS Extract, which can be used for GEDmatch/Admixture Studio and Global 25, which is much better for both than 23andMe v5.

If you want a cheap option without waiting for offer periods, YSEQ's H-L901 SNP pack and mtComplete services together is your best bet outside of offer times ($233 together w/ free shipping), however I would recommend waiting, if you can. You could pay $14 more for mtDNA sequencing from FTDNA if you really wanted access to their mtDNA matching database but YSEQ's Y-SNP pack is my recommendation for getting an accurate subclade results outside of WGS.

One of YSEQ's owners has stated on Facebook that they're working on the currently expensive prices of YSEQ WGS, so that could be something to keep your eyes peeled for. I'm personally looking forward to seeing how things go here, as YSEQ is a fantastic company that has a very strong reputation for being quick, helpful and relatively head-ache free, especially compared to Dante.

If you really wanted FTDNA matching, you can order a Y12 from FTDNA later down the line and upgrade to Y37, or just go straight to Y37. There are not that much South Asians on their database compared to Europeans, so the most I would recommend in terms of STR's from them is Y37. I don't have any Y25+ matches on there but common SA lineages like R1a and H should have more people in their database.