Y-sequences are sources for Y-SNP variation and Y-Phylogeny refinement (tree/pedigree). Summaries/Collections of Y-sequence positions in J2-haplogroup:
- tree.j2-m172.info: Tooltip/Hover has (terminal) sample info or view data tables.
- yfull.com/tree/J2: phylogenetic listing and linking of 1000 Genomes samples
- docs.google.com/spreadsheet/… Public “whole genome” chrY data analysis: listing and further info of 1000 Genomes and Personal Genome samples
- http://gdriv.es/j2a-m410: J2a phylogeny research diagrams with indication of 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.
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:
- Read/alignment raw data (.BAM files):
- 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
- 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
- ancient DNA J2 samples see Scientific Papers;
- Variants and coverage data (.VCF + .BED, CGI/CGA):
- 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
- Personal Genome Project (USA/Canada/international, low-coverage, ongoing, CG data, 3 J2a)
- Hallast et al 2014 (PH-SNPs): SNP lists and vcf for ca. 3.5 Mb high coverage, CG, Dec. 2014.
- Known variants status and novel variant data lists (.CSV, etc.):
- Shared and sample variant data lists (.CSV, etc.):
- Shared variant data lists (.CSV, etc.):
- Known variants status (.CSV, etc.):