Genetic Homeland DNA Marker Index For Y4580 On Y Chromosome

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• 1Numeric position values based on human genome assembly hg38, Genome Reference Consortium Human Reference 38 (GRCh38.p7, 2016). For MtDNA, hg38 FASTA file is GenBank reference sequence J01415.2 / NC_012920 based on the Revised Cambridge Reference Sequence (rCRS) from MITOMAP The Reconstructed Sapiens Reference Sequence (RSRS) has same position coordinates as hg38 but some allele differences. RSRS FASTA reference file is available from Behar et al doi:10.1016/j.ajhg.2012.03.002.
• 2Numeric position values based on human genome assembly hg19, Genome Reference Consortium Human Reference 37 (GRCh37, 2012) aka NCBI 37. hg19 FASTA file was GenBank reference sequence NC_001807.
• 3Numeric position values based on human genome assembly hg18, Genome Reference Consortium Human Reference 36 (GRCh36, 2006) aka NCBI 36.
• 4Numeric position values based on provisional Y chromosome assembly from GenBank entry CP086569.1
  • 62,456,832 base pairs, published Nov 16, 2021
  • Corrected Jan 14 2022 by Thomas Krahn
  • Replaced by assembly CP086569.2 below.
• 5Numeric position values based on provisional Y chromosome assembly from GenBank entry CP086569.2
  • 62,460,029 base pairs, published Apr 04, 2022
  • Sample from participant huAA53E0 in the Personal Genome Project. Also designated NA24385 (Coriell ID), HG002 (NIST ID), CP086569 (GenBank), GM26105 (stem cell from LCL), and GM27730 (PBMC), and Ash1.
  • Same sample & sequencing data used for Y-chromosome portion of the T2T-CHM13 v2.0 reference genome (but not for other chromosomes). T2T CHM13 is the foundation of the future human pangenome reference genome (aka hs1 ).
  • An Ashkenazi male (GCA_009914755.4) who is phylogenetically a descendant of Y-DNA haplogroup J1-M267
• 6Numeric position values based on provisional Y chromosome assembly from GenBank entry CM034974.1
  • 62,480,187 base pairs, published Apr 12, 2022
  • Sample also designated HG01243 (Coriell ID), CM034974 (GenBank), GCA_018873775.2 (assembly), SAMN13957917 (BioSample), and PR1 (genome).
  • A Puerto Rican native who is phylogenetically, a descendant of Y-DNA haplogroup R1b-DF27 and its subclade R-FT51793. Autosomally, individual is said to have significant African ancestry.
• 7Ancestral (also abbreviated as Anc) refers to the DNA allele at this position prior to the mutation event occuring. While many tend to think of the hg38 Reference Sequence for the human genome Ref allele values to be the same thing as the ancestral allele, that is not always the case as the hg38 assembly itself is a composite of several genomes from haplogroup R1b and thus is not purely based on historical descent (phylogeny).
  • An entry of ins means this mutation is an insertion of new base pair(s) and so there was no ancestral allele.
• 8Derived (also abbreviated as DER and Alt) refers to the DNA allele observed at that position after the mutation event.
  • An entry of del means the ancestral allele was deleted.
  • Note that for insertion and deletion DNA mutations, the Genetic Homeland DNA Marker Index strives to identify the position at which the mutation actually occurs and what the actual gained or lost base pairs are. However, some labs are reporting the position and allele value of the base pair preceeding the mutation and then including that base pair in both the Ancestral and Derived allele sequences.
    For Example:
    • FTDNA enumerates mutation BY394 at hg38 position 14897133 described as TA to T mutation.
    • Genetic Homeland enumerates BY394 at hg38 position 14897134 with A to del mutation - because the T allele at position 14897133 did not actually change in the persons in whom BY394 was detected.
• 9RSID is an abbreviation for Reference SNP ID number, or "rs" ID. It is an identification tag assigned by the United States National Institute of Health (NIH) National Center for Biotechnology Information NCBI to a group (or cluster) of SNP markers that map to an identical location. As the Human Reference sequences are updated, the chromosome position of a particular mutation may change, but the RSID should stay the same.
• SNP stands for single nucleotide polymorphism.
  • SNP Name Prefixes: The letter prefixes of the Y-chromosome SNP labels typically represent the laboratory or entity which identified or published the SNP marker.
    • BY, FT, FTA, FTB, FTC => Family Tree DNA laboratory
    • L => Thomas Krahn at FTDNA, primarily from his Walk On the Y project there
    • A => Thomas Krahn at his YSeq laboratory
    • Y => YFull Team (Russia) YFS and YFC are SNP candidate names YFull uses as preliminary designation for new mutations under study
    • FGC and FGCLR => Full Genomes Corp
    • Z & DF => ISOGG or wider genetic genealogy community
    • M => Stanford University and other academic researchers
    • MF => 23MoFang ( 二十三魔方生物科技有限公司 ) - a Chinese genetic genealogy testing lab company
    • MV => Unknown who originates these designations but they appear on 23MoFang tree.
    • CTS => Chris Tyler Smith who recorded many Y mutations using 1000 Genomes Project data.
    • S => Jim Wilson (aka Jim Flett Wilson), University of Edinburgh and formerly Britain's DNA
    • ABR => Adam B Rohrlach, Max Planck Institute
    • TY => TheYTree.com ( 祖源树 ), a Chinese-based, DNA analysis service associated with WeGene ( 微基因 - Shenzhen Zaozhi Technology Co., Ltd) and YooGene ( 源基因 - Shanghai Sapiens Biotechnology Co., Ltd ).
    • C => DNAChron (Tianjin Shangyuan Gene Technology Co., LTD ) - a Chinese-based, DNA analysis service. Note that their Mutation Info position seems to use the CP086569.2 assembly.
    • KHU => Abdulrhman Alkhusaili a Saudi Arabian researcher. KHU Tree SNPs
    • DC => Dennis Wright of Australia - DNA Project Leader and independent researcher focused on Dal Cais associated lineages from Ireland
    • BTL => Brad Larkin - DNA Project Leader, founder of GeneticHomeland.com, and independent researcher
    • For another list of SNP label prefixes, see the bottom of the ISOGG Tree page
  • The numbers following the prefix are typically just a discovery sequence number and have no biological meaning.
• Decimal Suffixes on SNP names such as .1, .2, etc indicate that a mutation to the same altered state at the same chromosome position has occurred multiple times and so the suffixes distinguish between mutation instances. For instance, a T->A mutation occurred at position hg38:13875193 in an ancient person with with DF21 and is referred to as Z3006.1 so as to distinguish it from another T->A mutation at the same position which occured later in a person who was not DF21. The 2nd instance we refer to as Z3006.2. The decimal suffix approach is superior to the compound haplogroup-mutation approach as the same mutation can and does occur multiple times within the same major haplogorup. e.g. R-S6932 (hg38:13061053-C-T) has been found to occur under both R-U106 and R-P312.
• Underscore Suffixes on SNP names such as _1, _2 indicate instances where the same mutation has been reported at different chromosome positions. This phenomenon occurs most often when the mutation occured on an unstable region of DNA called a pallindrome where the entire region may have shifted.
• pseudoautosomal regions PAR1 and PAR2 are portions of the Y chromosome which undergo recombination with the X chromosome and so should not be relied upon for patrilineal ancestry markers in the way that SNPs on the non-recombining portion of the Y chromosome (NRY) are used. This database is primarily focused on the NRY. However as some labs are reporting Y mutations from the PAR1 and PAR2 regions of the chromosome, some PAR-region markers may be included here. We have endeavored to annote a warning on any markers listed here in these regions.
  • PAR1 spans hg38 Y position 10,001 to 2,781,479
  • PAR2 spans hg38 Y position 56,887,903 to 57,217,415
• MtDNA stands for Mitochondrial DNA. Within MtDNA Reconstructed Sapiens Reference Sequence (RSRS) marker system is presented along with the Cambridge Reference Sequence (rCRS or CRS) and Yoruba nomenclature.
• van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. http://www.phylogree.org. doi:10.1002/humu.20921 Updated to PhyloTree mtDNA Build 17 (18 Feb 2016)
• STR stands for short tandem repeats.
• Genetic markers attributed to Academic List or academic study came from lists of SNPs provided by academic researchers such as Dr. Toomas Kivisild. If you want to find the original research paper, try using Google Scholar to search for papers that mention the ethnic group, chromosome and/or haplogroup you are looking for.
  • e.g. Google Scholar query for DNA haplogroup B5 Y chromosome
    • If looking for a particular mutation, be sure to to comb through the supplemental material and tables of the paper as individual mutations are rarely named in the text of the main research paper.
    • Also try searching the supplemental material for the hg192 positions, as individual SNP labels (such as FTxxx) are usually not present in academic papers and most academic papers do not yet use hg381 positions in their work (as of 2021). That is why GeneticHomeland.com strives to show all the cross-referenced chromosome labels and positions here!
  • Also see our News page which typically describes the date and source of major SNP data loads.
  • You can also hire a professional genetic genealogy researcher to do this for you at LegacyTree Genealogists