YFull review – Ancestry analysis made easy?

YFull Review Summary

YFull is an upload site for Y chromosome and mitochondrial DNA sequencing data that provides deep ancestry analysis. Learn more in our YFull review!

Nebula Genomics

Results
Price
Comprehensiveness

Summary

YFull analyzes Y chromosomes and mtDNA at a reasonable price. However, information is limited to those sections of the genome.

4.3

7 Facts from our YFull Review

  1. Location: Barcelona, Spain
  2. Services: DNA data upload and interpretation of Y-DNA and mtDNA
  3. How it works: Upload raw DNA data from other companies as a BAM or VCF file to receive reports
  4. Reports: Y-DNA and mtDNA interpretation
  5. Privacy: No sharing of data with third parties without consent 
  6. Cost: $49 for Y-DNA analysis, an extra $25 for mtDNA analysis
  7. Complementary services: Nebula Genomics (30x whole genome sequencing, including Y-DNA and mtDNA)

This review is written with the intent to be as unbiased as possible. However, it represents the opinion of an individual reviewer and is therefore subjective. Furthermore, at Nebula Genomics we seek to educate the public about the benefits of Whole Genome Sequencing. Information about our Whole Genome Sequencing DNA test is therefore incorporated into the review.

September 9, 2022

Edited by Christina Swords, Ph.D.

Pros and Cons

Pros

  • No billing until results are ready
  • No subscription fees
  • Extra information about your private variants. 
  • You can compare the results across different NGS or full genome tests taken
  • YFull Groups can display and compare all STRs 
  • You can find SNP matches in YFull Groups for any named or unnamed variant
  • You can contact other members and the group administrator in your YFull Groups
  • Questionable SNPs or STRs from your NGS test can be verified at YSEQ and added to your results
  • The platform supports mtDNA sequencing interpretation

Cons

  • STR analysis is given less priority than SNP analysis and takes several weeks to complete, delaying the receipt of interpretation results
  • YTree updates monthly

YFull Introduction

YFull is an upload site for Y chromosome and mitochondrial DNA sequencing data. The service also provides advanced ancestry analysis. Among other offers, it promises to “unlock your terminal haplogroups and known Y-SNPs.”

Single nucleotide polymorphisms, or SNPs (pronounced “snips”), are differences in DNA sequences at the level of individual base pairs. In essence, a SNP is a difference in a single DNA block (nucleotide) among people. 

On the other hand, short tandem repeats, or STRs, are a series of repeated DNA sequences (A, T, C, or G) that differ between individuals. Identifying the number of repeats in specific areas of the genome can create a “DNA fingerprint”. Professional and amateur genetic genealogists may use this fingerprint to investigate an individual’s ancestry. 

Together, SNPs and STRs are markers that can be inherited. The combination of such markers is known as a haplotype. Different Y-DNA and mtDNA tests for different haplotypes may assign individuals to a specific “haplogroup”. While Y-DNA tests can tell us more about paternal line, mtDNA tests tell us about maternal lineages. 

You can use YFull to look up everything down to your terminal subclade, the most specific branch of your haplogroup.

YFull started in 2013 in Moscow, Russia with the specific purpose of interpreting Y-chromosome sequences. It is important to note that this is not a DNA testing company. Instead, it is an analysis company offering next-generation sequencing interpretation for Y-DNA and mtDNA.

In addition, the company offers convenient visualization of DNA results and a detailed, public haplogroup Yfull tree for you to compare your “path of mutations” with other samples in YFull’s database. 

The original team consisted of Vadim Urasin, who has been an active participant in the DNA genealogical community since 2008. Other members of the original team include Vladimir Tagankin, the DNA database “semargl.me” developer, and Roman Sychev, a moderator on dna-forums.org. 

Want complete Y chromosome and mtDNA sequencing data to use with YFull?

Nebula Genomics offers 30x Whole Genome Sequencing! Click here to learn more!

How to Upload your Data to YFull

Let’s start the YFull review with an overview of the service. 

A chart detailing which features are reported in NGS interpretation for VCF and BAM files
A chart detailing which features are reported in NGS interpretation for VCF and BAM files

To order a YFull test analysis, users must upload raw data from other genetic testing providers. Your file can be from several companies, including Nebula Genomics. You can cross-reference kit numbers related to YFull IDs for easier access. The data can be a .BAM/.CRAM or .VCF.

One caveat – data extraction from .VCF files will be incomplete (about 50-70%). If a user uploads a .VCF fie, STR matches will not get reported. YFull does not accept data in FASTQ format. Therefore, optimal results require the upload of a .BAM file.

Finally, customers can create a username when placing an order. They do not need to pay at the time of ordering. 

Screenshot of YFull order page with list of what it includes, a form, and an order now button
YFull order page

After several weeks, the results will be ready and available after paying $49. You can purchase an mtDNA interpretation at an additional cost of $25.

A chart detailing which features are reported in NGS interpretation for mtDNA
A chart detailing which features are reported in NGS interpretation for mtDNA

Review of YFull Reporting

As mentioned earlier, there are two types of Y-DNA mutations: SNPs and STRs. Both types of mutations are useful for probing for different reasons. YFull offers an analysis of both SNPs and STRs. 

Screenshot of a YFull page section featuring three hyperlinked squares
YFull customer homepage

According to YFull, there are 185,780 known positive SNPs and 780+ known STRs. Additionally, 1,482,319 novel variants that have not been discovered before. 

List of known SNPs
List of known SNPs

The known SNP report shows the customer’s position on the Y-haplotree and the SNP results for all SNPs tested on the customer’s tree branch. Details include lists of SNPs in adjacent tabs, highlighting “ambiguous” SNPs and no call SNPs (i.e., SNPs that were not determined during the process of genotyping a person’s DNA). 

YFull list of novel SNPs
YFull list of novel SNPs

We can also view a list of novel or private SNPs. These novel SNPs are stratified by quality (e.g. Best, Acceptable, Ambiguous, Low, One Reading).

All private SNPs have a YFS prefix. The red checkmark next to some of these SNPs means that they can be verified through YSEQ. The G refers to the location of this gene within this SNP. 

Table with many small columns titled with nitrogenous bases (A, C, G, T) and rows filled and partially filled in
Aligned sequencing reads

The report also shows insertions and deletions (indels), which are positions in the sequence that have extra nucleotides. 

List of indels
List of indels

Moreover, one can access SNP matches. These are SNPs shared or assumed to be shared with other samples in YFull’s database. You can trace these SNPs back to a distant common ancestor.

The database will continue to compare a sample as it updates. If any of these private SNPs match newly discovered YFull samples, these SNPs will get names in the Y-series. 

Table with SNP matches in a table with nine visible rows, featuring the country of origin, YFull ID, and shared SNPs columns
YFull close DNA matches

One can also observe individual SNPs to get more information. This includes the number of reads that overlap that SNP, reference sequences, and so forth. 

Section of a table with several rows with some information on base pairs
YFull search in a BAM file

There is a useful feature to allow customers to query results by SNP name. 

Screenshot of a row describing an SNP
YFull SNP query feature

We close our review of YFull reporting with a look at the YReport feature. YTree includes family tree DNA haplogroups and shared SNPs (Y-SNPs) in every haplogroup project. It is based on public sample data, including the 1000 Genomes Project.

YTree gets updates almost every month based on submissions from haplogroup experts, the International Society of Genetic Genealogy (ISOGG), and others. The list of SNPs from the root to the terminal haplogroup is sharable. 

Graph in a waterfall-like format featuring green squares with letters representing chromosome positions
YFull YTree
Table listing several positions, their SNPs and subclades
YTree statistics

Customers can also observe STR results (780 that are tested), matches, and variants in the common 12, 25, 37, 67, & 111 format.

Table with six rows of SNPs and information in columns of rectangles with SNPs and numbers in them
YFull STR marker results

Additional features include haplogroup age estimates based on a 2015 study where authors outline an original method of selecting true mutations. If a customer’s raw data includes mtDNA sequencing, the report will list mtDNA haplogroups based on PhyloTree. In March 2019, the platform introduced mtDNA analysis for an extra fee.

Other services include:

  • Statistics, such as BAM file size, mapped reads, length coverage, median depth coverage, and more (in the YReport)
  • CSV files (comma delimited files) for known SNPs, novel SNPs, and known STRs
  • The ability to browse raw data by position (genome builds hg19 or hg38)
  • My news: a chronological listing of changes to YTree since your YFull sample (upon updates)

Review of YFull Privacy

The website’s privacy policy states that “YFull.com respects your privacy and will not disclose your personal information without your consent” unless required by law.

The terms and conditions do not mention any exceptions with third parties. This is not to say that it does not share with third parties, but the policy does not refer to it.

The personal information annex to the privacy policy discusses the variety of user data collected. This includes email address, ancestry information & raw genetics data, cookies, and IP address.

The YFull team has complete access to this data. Members of groups that the user has joined may have partial access to certain parts.

Citizen science and academic researchers may also use this data. This occurs when the user has given personal permission to participate in a study.

YFull stores your data on a server located in a secure data center in Moscow, Russia.

Google serves store some information, such as email addresses. You can delete your data and account by navigating to the “settings” page.

YFull Reviews

Several short reviews are on the company website. Other than that, there are not many accessible customer reviews online.

Nebula Genomics

We finish our YFull review, by looking at some complementary products.

Our data can be imported into YFull, giving access to an extensive Y chromosome and mitochondrial DNA database. Check out more of the blog to learn more about the importance of sequencing Y-DNA and mtDNA and paternity testing.

Other DNA upload sites you might want to check out are:

You can also look into FamilyTreeDNA (Big Y results that includes an STR test and a SNP test).

Did you like our YFull review? You can read more reviews on our blog, including a service called YSEQ. Also, check out our complete guide to the best DNA test kit and other home tests.