J2 Y-chr sequences


Y-sequences are sources for Y-SNP variation and Y-Phylogeny refinement (tree/pedigree). Summaries/Collections of Y-sequence positions in J2-haplogroup:

DTC Y-sequences

Y-sequencing DTC (direct to consumer) is available since 2013 (see comparison chart). The list is not updated often and maybe incomplete because of missing analysis. If you like to have a more updated list please contact the J2 team.

J2-M172_spreadsheet > NGS

Y-sequence data from public projects and research

Projects and/or research with the goal to sequence and publish the complete genomes or the Y-sequence of volunteers:

  1. Read/alignment raw data (.BAM files):
    1. 1000 Genomes Project (CTS & Z-SNPs): International, ca. 14 Mb low coverage, completed 2013, 42 in J2a and 21 in J2b – terminal position see YFull J2 (id:HG/NA) or 2014-01-18_J2a-M410_1kG_Phylogeny_v1.0b.pdf
    2. Lippold et al 2014 (Stoneking SK-SNPs): 51 pop., 0.5 Mb NRY, 33 J2 (Sep. 2014): NRY SNPs CEPH-HGDP, NRY sequencing data incl. BAM ENA PRJEB4417 – terminal position: SK sample list not finished yet
    3. ancient DNA J2 samples see Scientific Papers;
  2. Variants and coverage data (.VCF + .BED, CGI/CGA):
    1. Estonian Biocentre (Karmin et al 2015, B-SNPs): diverse pop., high coverage Y chr. CG (Jan. 2015, 8 J2a, 5 J2b) – terminal position: EBio J2 sample list
    2. Personal Genome Project (USA/Canada/international, low-coverage, ongoing, CG data, 3 J2a)
    3. Hallast et al 2014 (PH-SNPs): SNP lists and vcf for ca. 3.5 Mb high coverage, CG, Dec. 2014.
  3. Known variants status and novel variant data lists (.CSV, etc.):
  4. Shared and sample variant data lists (.CSV, etc.):
    1. Francalacci et al. 2015 (PF-SNPs): SNP lists for 23.1 Mbp (different numbers then 2013). Restricted genotype data access.
    2. Francalacci et al 2013 (PF-SNPs): SNP lists for ca. 8.9 Mb low-coverage data (831-905 in J2a). Restricted genotype data access.
  5. Shared variant data lists (.CSV, etc.):
    1. Genome of the Netherlands data (GoNL): 250 paternal lineages covered (2014), Y not included in online browser so far
  6. Known variants status (.CSV, etc.):
    1. BritainsDNA Chromo2 sample data (S-SNPs) for ~2000 European males was made available in Feb. 2014 (Y-SNP Positions)

Comparison