YFull – First Steps – ΑΝΤΩΝΙΟΣ ΔΝΑ PROJECT (2024)

Solve yourY-Chromosome Puzzle with Yfull!

Yfull is not a provider of Y-DNA or NGS tests, but an analysis service for NGS with a database in which data from NGS tests are compared and analyzed, regardless of the provider. This allows to compare the results of currently 13 sources. (Commercial companies and scientific studies) See: phylogeographer.com/yfull-cost-benefit-analysis. The results are presented in the form of a Y-tree in different representations. The kits are presented anonymously and the Y-tree (as well as the mt-tree) is publicly accessible for everyone. This makes it not only an enrichment for the submitters, but also for everyone who is concerned with the topic Y-tree (as well as mt-tree).

• Preparation: You don’t upload the raw data of the NGS test to Yfull yourself, but indicate where it can be downloaded. You can get the link from the provider where you did your test. (FTDNA, YSEQ, FGC). Companies like Dante Labs don’t offer such a link for Yfull directly, so you have to make the required file accessible via a cloud. You can find an easy instruction here: Prepare the BAM file for YFull.
• Go to the Yfull site and order the analysis for $49: https://www.yfull.com/order/
• The selection of VCF as raw data file type is only possible for FTDNA BigY. The preferred raw data file type is BAM. For other companies only this can be selected.
• Specify the testing company.
• Enter the URL to your BAM file.
• Under “Comment” you can send additional information to the Yfull Team. This is especially important if you send several kits from the same participant. (e.g. This is an upgrade of BigY-500 kit YF10815)
• Order Now!

You willreceive a confirmation email immediately:

Hello! Your order will be verified by the manager. If the raw data link is correct, youranalysis will be batched. Login and password for new clients to access the sitewill be sent. Notification for payment will be sent after completion of theinterpretation. Thanks.

2.1 The SNP Analysis –Donated Kits

Now we haveto wait. If the link works, the analysis is batched and you get access data andthe “YF number” for the kit. This can take some hours, but also a fewdays. The payment, which unlocks all functions, will be done *after* the analysis.

Some dayslater the kit is placed in the Y-tree with a temporary position. The YF numberis grey and a small box with “new” is located behind the kit. Theexact position is only obtained after the analysis and the update of the tree(the analysis takes about four weeks).

2.1.1 Settings:

Now, youcan and should make some settings. (Button “Settings”, top right).

Account Settings:

• COUNTRYOF ORIGIN = place of origin of the most distant known ancestor in the paternalline (Tab Y).
• MOSTDISTANT ANCESTOR = most distant known ancestor in the paternal line (Tab Y).
• USERNAME= Name of the user or nickname for this kit. This information makes it easierto choose if you administer several kits or participate in groups.

Sharing Settings:
Here you can share the results with Yfull users. This is especially interesting if you want a friend to explain the results to you. To share the results with another Yfull user, send an invitation to the email address with which the participant is registered at Yfull.

2.1.2 Useable functions atthis stage:

Twofunctions can be used while waiting for the results. “Browse rawdata” and “Statistics”.

With“Browse raw data” you can examine the raw data and query individualChrY and ChrM positions. With some practice and knowledge of the novel variantsof the other participants, you can determine your terminal SNP. (This functionis comparable to function 3.1.4 Check SNPs)

On“Statistics” you get a small statistic regarding the quality of theraw data. The figure shows thestatistics of two men (TMRCA 50 ybp). Big Y-500, same man upgrade to Big Y-700,fifth degree cousin WGS at Dante Labs.

2.1.3 Unlock results, or“Donate Kit“.

After aboutfour weeks the first part of the analysis is finished and you can have theresults unlocked with payment. There is also the possibility to“donate” a kit. Here only the SNP analysis is performed, without STRanalysis, and the kit does not participate in the age estimation. I personallysee no reason to do this, as I am interested in the complete analysis. However,it is a benefit for the Y-tree and the projects if people with limited interest(e.g. WGS testers with focus on health) submit their kits that way.

Afterpaying the one-time fee of $49, all functions are unlocked and the STR analysisand age estimation is initiated. The STR analysis will take a few days, orweeks. The age determination is done just before the next update of the tree,so this may take a few weeks. All other functions are available immediately,but you should be aware that there will be some changes regarding the new SNPsuntil the next update of the tree.

2.2.1 Uploading STR values

If you have performed a Y-STR test in addition to the NGS test, for FTDNA or YSEQ, you can upload the STR values. https://www.yfull.com/ls-upload-strs/ STR values that cannot be extracted from the NGS raw data are added in this way.

2.2.2 Uploading the MT FASTAfile

A WGS contains the entire mtDNA in addition to the entire Y chromosome, so that mt is added to the Yfull mt tree. If you participated with an NGS without mtDNA, you can upload your FASTA file additionally. https://www.yfull.com/mt-upload-list/

You can andshould now make some settings. (Button “Settings”, top right).

Account Settings:

• COUNTRYOF ORIGIN = place of origin of the most distant known ancestor in maternal line(tab mtDNA)
• MOSTDISTANT ANCESTOR = most distant known ancestor in maternal line (tab mtDNA).
• USERNAME= Name of the user or nickname for this kit. This information makes it easierto choose if you administer several kits or participate in groups.

2.2.3 Join YFull Groups

Check out the list of Yfull groups at https://www.yfull.com/groups/list/ and join the group that matches your haplogroup.

2.3 Positioning in theY-tree

You only get a preliminary position. After successful SNP analysis and update of the tree you get the next “Preliminary” position. Which positions you can take has already been described in NGS – Take part in the Y-Tree. The final position in the Y-tree is “never” obtained, because the Y-tree “lives”. With each additional kit on the relevant clades, the shape of the tree can change.

It is worthhoovering the mouse pointer over the Yfull interface and experiencing foryourself what information and links are connected behind the buttons.

3.1 SNPs

3.1.1 Hg and SNPs

This listsall SNPs that have tested positive, are likely to be positive, or are No Calls.The green box shows your terminal SNP, or the name of the block of yourterminal SNPs (here I-Y158862). Below it, all terminal SNPs of this block arelisted in sequence (here A23501/BY182855 and BY182587/Y158862).

Under“Known SNPs”> Positive, all SNPs are listed that have testedpositive with this kit and are “known”. These are the SNPs that havebeen found in other kits before. Yfull evaluates the quality of these SNPs withan internal star system.

Figure 2shows what this view looks like just before new branches are formed.
Y158878 • BY183648, level I-Y158878, terminal new, five stars.

• Y158878and BY183648 are two different names for the same SNP.
• LevelI-Y158862 indicates the block to which this SNP (still) belongs.
• “Terminalnew” indicates that something is going on. These SNPs have only recentlybeen shared with another kit and were previously under “Novel SNPs”.After the next update of the tree, these SNPs will form the new block of terminalSNPs.
• Onlythe upper two SNPs have five stars rating. One of these two SNPs will probablybe used to label this new block.
• SNPswith the addition “private” are mostly low quality SNPs that havealready been found in several kits, before.
• Ifyou click on the magnifying glass in front of the SNPs, you will see a viewwith more information about the respective SNP in a kit. (see 3.1.4)

3.1.2 Novel SNPs

The Novel SNPs are SNPs that are only found in your kit. They are divided into five categories. “Best qual” and “Acceptable qual” have very good or sufficient quality. “Ambigous qual” and “Low qual” have only moderate quality. You cannot be sure that these are actually positive, because they have either not been read often enough or do not show clear results. It is recommended to make them orderable at YSEQ with “Wish a SNP” and to check them for correctness. More about this topic here: Verify relationship in paternal line, with known terminal SNP and private „novel“ SNPs from NGS

SNPs thatcan be ordered at YSEQ are marked with a small sign at Yfull. If this signappears orange, this has never been tested positive, before. A green signstands for SNPs that have already tested positive. Hoover the mouse over this signto see how often it has been tested.

If youclick on the magnifying glass in front of the SNPs, you will see a view withmore information about the respective SNP in a kit. (see 3.1.4)

Clicking onthe blue “.BAM” field opens a Y-Browser.

3.1.3 SNP Matches

This viewshows the SNP matches as they are also shown on the Y-tree, but you get somemore information about the user. Firstly, the “Most Distant Ancestor”and secondly, the information which SNPs you actually share and which SNPs youonly ambiguously share.

3.1.4 Check SNPs

Thisfunction is similar to the previously mentioned “Browse raw data”.However, here you can enter the name of the SNPs. On the right hand side youcan see immediately whether the SNP has been tested positive or negative. (Thegreen sign behind I-L38 stands for “Verified by Sanger Sequencing, YSEQtested”).

If youclick on the magnifying glass in front of the SNPs, you will see a view withmore information about the respective SNP in a kit.

Here you can find out the ChrY position (Hg19) and (Hg38) for this SNP, as well as in which area of the Y chromosome it is located. “Reads” indicates how often this was read.
The ChrY position (Hg38) for L38 is 13556190 in the region of Yq11.221. This was read 38 times in this kit and resulted in 38 times “G”. The reference has “A” at this point. The known SNPs at this position are S154/L38 from A to G, “Verified by Sanger Sequencing, YSEQ tested”, 5 star rating, YF= in Yfull database, YB=in ISOGG YBrowse database.
Reference sequence (100bp) shows which values the reference has 50 bases before and 49 bases after this position.

3.1.5 Age Estimation

The age estimation of a clade is based on the positive SNPs of all samples. On the overview you can see the influence of your own kit on the age estimation of all samples. In the other tabs you can see which SNPs were taken for the age estimation and which ones were not taken and why. A detailed description of the method can be found by following the link below the table. What is YFull’s age estimation methodology?

3.1.6 Upgrades

There aretwo upgrade options. This applies *only* to differently prepared raw data ofthe same test. (An “upgrade” from Big Y-500 to Big Y-700 is not anupgrade, but a new test)

• Upgradethe analysis of a Big Y, from raw data format VCF to BAM. This upgrade is freeof charge and is recommended, as only the BAM contains all information for acomprehensive analysis.
• Upgradeof the analysis from a NGS, from Hg19 to Hg38. This upgrade is possible, butYfull does not recommend it.

For eachupgrade you do, you get a comparison of the results for:

• Known SNPs
• Novel SNPs
• STRs
• Statistics

3.1.7 Comparisons

If a personhas performed several tests, e.g. Big Y-500 vs. Big Y-700 or Big Y-500 vs. WGSYSEQ, the results can be compared here. These are:

• KnownSNPs
• Novel SNPs
• STRs
• Statistics

3.1.8 YReport

This is anoverview of all positive SNPs of a kit from the Y-Adam, up to the tester. Youcan see at a glance which SNPs have been read, which are No Calls or“Ambigous”. Selecting the SNP shows us the window, which we alreadyknow from 3.1.4, with the values for this SNP.

3.2 STRs

The rawdata from NGS not only contain information on SNPs. Yfull can read out up to780 STRs and offers some nice additional features.

3.2.1 STR results

The 780STRs are listed here. The different colours of the boxes, stand for:

• White= reliable STR
• Grey= uncertain STR
• Blue= STR taken from YSEQ or FTDNA file

You candownload this file as .CSV.

3.2.2 STR matches

Matchesbased on STRs are listed here. For this purpose, the STRs that differ in thekits are simply summed up. About sense and nonsense of this representation onecan argue. I do not find it informative.

3.2.3 STR Variants

However,this function is very informative. Here you get the mutation course of yourSTRs from Y-Adam to yourself. They are sorted from “young” to“old”, linked to the information within which SNP blocks they aremutated.

For abetter overview, the figure shows only the selection for Y111. The first columnshows the label of the SNP block in which the STR is mutated. Next to the STRyou get the information which other kits share this STR with you. On the rightyou can see values for:

• Thedetection rate – In which part of all kits was this STR detected?
• Themutation rate – Five stars stand for an STR which rarely mutates. The fewerstars, the more likely this STR tends to mutate, so that two kits can randomlyhave the same value.
• Ancestral(ANC) and derived (DER) value for this STR.

This viewcan help you to understand the order of STR mutations. Under certaincirc*mstances, subgroups can be formed based on STR values, where nodistinction is possible with SNPs. However, caution is advised, especially ifthe mutation rate is low.

STRs with amutation rate of five stars and sufficient samples are actually used to formsubgroups with YFull.

3.3 Contacting YFull users

If you area user of Yfull you can contact any other user. After clicking on “Newmessage”, simply enter the number after “YF” as“Recepient” (arrow 3).

Check out the list of Yfull groups at https://www.yfull.com/groups/list/ and join the group that matches your haplogroup. This allows you and the administrators of the group to conduct research within the group.

4.1 Y-Browser

With the Y-Browser you can compare values for individual Y-Chr HG38 positions of the group users. You can also compare positions like “Novel Variants”, which is not possible with the “View SNPs” of “Y-Results”. This way you can see at once if there are test persons who have no calls for these positions and could theoretically be positive for these new SNPs. In case of increased suspicion (e.g. common STR mutations) the new SNPs can be tested on these test persons after wishing the SNPs with “Wish a SNP” for being orderable.

4.2 Y-Results

4.2.1 Y-STR Group viewer

With“View Y-STRs (classic)” and “View Y-STRs (coloured)” youget a table with the 780 STRs of all group members.

• “ViewY-STRs (classic)” shows a classic view. It contains the information aboutthe reliability with which a STR (reliable or uncertain) was extracted.
• “ViewY-STRs (coloured)” shows the modal values, minimum values and maximumvalues in colour. Here the information regarding the reliability of the STRs ismissing.
• Thistable can be downloaded and used for STR investigations.

4.2.2 SNPs Group viewer

Thisfunction is similar to the Y-Browser, but has the advantage that you can enterthe SNPs directly. Therefore you cannot select “New SNPs” here. Youcan immediately see which SNPs have *not* been tested with which testers (NoCalls). So you can find potential candidates for not yet discovered subgroups.

In theexample in Figure 12, the SNPs of block Y177573 were queried. Most of the SNPswere read out for all participants. SNPs Y177575 were only read in two kitswith WGS and one Big Y-700, out of a total of four Big Y-700. SNP Y177577 hasonly been read by two WGS (green and red arrow). For the participants with BigY these are No Calls. One could now make these two SNPs orderable at YSEQ with“Wish a SNP” and then check if the kits ofY125026* are positive for them.

This isalso one of the reasons why I prefer a WGS in comparison to a targeting NGS likeBig Y. The better coverage and therefore hardly any no calls. (see fig. 1)