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YFull

From ISOGG Wiki

YFull
Type Sole proprietor
Industry Genetic genealogy
Founded 2013
Founder(s) Vadim Urasin
Headquarters Moscow, Russia
Area served International
Products Y-DNA NGS Sequencing, Interpretation (SNPs, STRs, Phylogeny)
Website yfull.com


YFull.com was founded in 2013 and focuses on the interpretation of Y-chromosome sequences. The main aim of the project is to provide services for the analysis of full Y-chromosome raw data (BAM) files and convenient visualization. The data is collected and analysed and newly discovered single-nucleotide polymorphisms (SNPs) are placed on an experimental Y-tree. Haplogroup and thematic projects are offered.

Services

Analysis of Y-DNA NextGenSequences raw data (BAM or FASTQ file). Technical requirements raw files: Alignment BAM file, Coverage for full reports is min 25X, Read length min 100 bp. WGS 4x, 10x, etc. is also accepted. [1]. After several weeks of raw data analysis the SNP results are ready and up to notification the payment of $49 is requested either with PayPal or trough Credit Card (over Assist accepting Visa, Mastercard, etc.). A month after the payment request unpaid results/samples will be hidden, STRs will not be processed (usually take over a month from payment date) and basic access ("Check SNPs", "Browse raw data" etc.) is not anymore available. Payment will unhide the results.

  • YTree: Haplogroups and shared Y-SNPs: listing under the terminal Y-haplogroup in the YTree and listing of all shared Y-SNPs in every haplogroup
    • YTree based on public samples including 1000 Genomes Project (ca. 1292 males, HG/NA IDs), Francalacci et al 2013 (ca. 1194 Sardinians, added since Nov. 2015, ERS IDs), some ancient DNA files for calibration and data of 4867 customers (version 4.01 Jan. 2016, mainly from FTDNA BigY and FGC Y-Elite testing, YF IDs).
    • regular YTree updates based on the amount of new samples that have done YFull analysis: ca. every month, YTree updates based on submissions of Haplogroup experts, ISOGG, etc. to cover haplogroups without two samples included in the YFull analysis, YTree Archive: archived versions starting with version 3.7 (March 2015), YBrowse SNP name synchronization on a daily basis (159,000 SNPs with 183,000 names in Jan. 2016);
    • SNP matches: Shared SNPs and Assumed Shared SNPs to nearest available samples limited to an estimated TMRCA of 2500 ybp or younger.
  • Haplogroup age estimates based on the Adamov et al 2015 study a Y-SNP counting in the combBED area (parts of the Y-Chromosome expected to be stable in the mutation rate) is applied to calculate formation and diversification (TMRCA) of haplogroups including 95% CI error ranges.
    • age estimates are updated when new samples are included (together with YTree).
YFull - Statistics Screen 2016-02-14.
  • Private / Novel SNPs: Y-SNPs found so far only in your YFull sample (checked against over 71k known Y-SNPs).
    • Comparison is done automatically and with all other YFull samples including 1000 Genomes samples.
    • If a new YFull sample shares some of those Y-SNPs with your YFull sample those are given names in the Y-series and your Novel SNPs list will be updated (together with YTree)
  • Y-STR results: All known (over 490) short tandem repeats values are extracted from the Y-chromosome (if covered in the data) and are provided. The markers are displayed alphabetically online, but are also available as a comma separated variable (CSV) file as a download. The markers in the CSV file are arranged in the widely used FTDNA formatting (12, 25, 37, 67, & 111). Not all of the STR markers at the 37, 67, and 111 levels, however, are available in the results. STR Analysis has a lower priority then SNP analysis and takes several weeks more to complete.
    • STR matches: Close matches and Distant matches based on "infinite alleles model" are listed
    • STR variants: STR value changes (mutation period prediction) for every ancestral haplogroup including the private STR-mutations. Included are a Mutation rate rating and stats about marker STR values for the main haplogroup as well as for all haplogroups. See FAQ.
  • mtDNA-Haplogroup: if the raw data includes mt sequencing the mt-Haplogroup in rCRS and RSRS format based on PhyloTree is listed.
  • Online Services: all the previously listed data is provided online as well:
    • CSV-reports (known SNPs, STRs, novel SNPs)
    • Browsing of raw data (BAM file) by entering position (hg19)
    • Check SNPs by entering the name
    • Statistics: ChrY BAM file size, Mapped reads, Length coverage, Median depth coverage, Positive SNPs, etc.
    • YReport: sharable list of all SNPs from the ROOT (Y-Chromosome "Adam") to the own terminal haplogroup
    • My news: chronological listing of changes in YTree concerning your YFull sample
  • Groups: similar to FTDNA projects GAP and group functions are provided facilitating manual comparison and analysis.
    • Y-SNPs: comparison table between group members by entering SNP name/s (comma-delimited)
    • Y-Browser: comparison table between group members by entering Y-Chr positions hg19 (comma-delimited)
    • Y-STR: comparison table between group members of all values or in 111, 67, 37, 25, 12 FTDNA format
    • Messaging: YFull kits can be contacted with a message system by using the numerical kit number part (after YF without 0): http://yfull.com/messages/pm/ID-NUMBERS/

Team

  • Vadim Urasin (aka Wertner): active participant of the DNA genealogical community since 2008, the developer of robots to collect Y-data from public sources, "Y-predictor" developer, FTDNA group administrator, developer of the Y-series SNPs (for R1a, J2b, R2a, Q, O etc).
  • Vladimir Tagankin (aka Semargl): active participant of the DNA genealogical community, the DNA database "semargl.me" developer, FTDNA group administrator and co-administrator, developer of the Z-series SNPs (for R1a, I, J2b), developer of the Y-series SNPs (for R1a, J2b, R2a, Q, O etc).
  • Roman Sychev (aka Maximus Centurion): active participant of the DNA genealogical community since 2006, since 2007 as moderator dna-forums.org (aka Maximus), molgen.org, FTDNA group administrator, developer of the Z-series SNPs (for R1a, I1, J2b), developer of the Y-series SNPs (for R1a, I, R2a, J2b, Q, O etc).

Blog posts

External links

References

  1. Vadim Urasin, 2015-12-06, YFull Facebook group: https://www.facebook.com/groups/yfullcom/permalink/556634711161738/?comment_id=561019407389935&comment_tracking={%22tn%22%3A%22R0%22}