Haplogroup R and Subclades

DNA Helix

A collection of Next Generation Sequencing, Chromo2, and individual SNP tests. Each group section includes samples known to have at least a single SNP tested downstream. Calls are indicated by a plus, minus or tilde. The tilde (~) calls represent a region reported covered in a Big Y BED file. Under most circumstances these are ancestral (-) calls, but they must be individually checked in the corresponding BAM file.

An experimental tree for the R haplogroup is now available for browsing.

Update (2016-07-04): GRCh38 lifted masterVAR files for PGP-Harvard and Estonian Biocentre sets have been partially restored. Deletion events and known reference calls are not yet included.

Mean NGS Callable Coverage by Test Type
Test Type Callable Loci combBED Loci Total Loci Samples (n)
1KG 6,534,873 (46.949% CV) 3,551,128 (48.967% CV) 21,891,635 (10.018% CV) 1131
Big Y 9,321,886 (6.747% CV) 7,695,860 (6.180% CV) 16,408,435 (5.939% CV) 425
WGS-Ancient 1,717,763 (195.279% CV) 1,096,692 (196.857% CV) 9,843,993 (90.156% CV) 5
WGS-FGC 14,851,489 (0.280% CV) 7,684,819 (2.019% CV) 23,292,235 (0.243% CV) 2
WGS-Veritas 15,355,763 (0.956% CV) 8,238,710 (2.227% CV) 23,622,049 (0.005% CV) 3
Y Elite 1.0 13,995,946 (4.715% CV) 7,904,207 (6.257% CV) 23,379,469 (2.168% CV) 31
Y Elite 2.0 14,270,887 (3.165% CV) 7,653,058 (6.797% CV) 22,445,261 (3.381% CV) 19
Y Elite 2.1a 13,895,496 (0.000% CV) 7,774,910 (0.000% CV) 20,965,083 (0.000% CV) 1
Y Elite 2.1b 13,257,518 (1.107% CV) 7,537,104 (0.698% CV) 20,674,303 (0.213% CV) 3