HumanGenomeDating
Atlas of Variant Age
Search
Examples: LCT, MCM6, EDAR, ZEB1
Shared Ancestry Database
TGP
1000 Genomes Project
Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
Watch movie
SGDP
Simons Genome Diversity Project
Populations: 130
Individuals: 278
Ancestry analyses:6,800,992
Watch movie
Shared Ancestry Movies
About
Bulk downloads
Frequently Asked Questions
Citation
Download profile data
for this variant in csv format
Share this page

Genealogical Estimation of Variant Age (GEVA)

Inference of the ancestral origin of a genetic variant at a single locus

Unmatched Variant ID, using internal ID instead:
X409559723
Alleles:
reference
C
–
alternate
T
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 2   position  109,559,723  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 97.7%
2.3%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 100.0%
0.0%
SAS 100.0%
0.0%
WEA 100.0%
0.0%
reference ← allele frequency → alternate
Select clock model
  Mutation clock
  Recombination clock
  Joint clock
Age estimation summary Joint clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP2,546.1 generations 94  =  1  +  931.000
Pairwise results table Joint clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Khomani_San-2A + S_Khomani_San-1A Concordant SGDP 109,471,639 – 109,830,597 358,957.5 0.47106700 56 550.1532 2,035.8
S_Khomani_San-1A + S_Masai-1A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 9 18.9455 9,501.0
S_Khomani_San-1A + S_Hungarian-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_French-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Estonian-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Saharawi-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + B_Sardinian-3A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Tajik-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + S_Lezgin-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + S_Jordanian-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + S_Luo-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + S_Saharawi-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + S_Luhya-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + S_Burmese-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + S_Mbuti-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_BedouinB-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Abkhasian-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + B_Yoruba-3A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + B_Mandenka-3B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + S_Esan-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Mandenka-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + S_Saharawi-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Piapoco-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-2A + S_BantuHerero-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Finnish-3A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Mozabite-1A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Greek-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Tubalar-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Icelandic-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Tubalar-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Masai-1B Discordant SGDP 109,559,712 – 109,568,400 8,688.0 0.00305908 4 7.6175 10,502.1
S_Khomani_San-1A + S_BantuTswana-2B Discordant SGDP 109,559,712 – 109,564,735 5,022.5 0.00256954 4 5.4664 14,634.8
S_Khomani_San-1A + S_Orcadian-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_BantuTswana-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Adygei-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Tlingit-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Ju_hoan_North-1B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Naxi-2A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + B_Mbuti-4B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Biaka-2B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + B_Dinka-3B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Mbuti-3A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 7 18.9455 7,389.6
S_Khomani_San-1A + S_Mende-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Mbuti-3B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Surui-1B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Mbuti-2B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 7 18.9455 7,389.6
S_Khomani_San-2A + S_Mozabite-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Mbuti-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Finnish-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + B_Australian-4B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_BantuKenya-1B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Mbuti-1B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 9 18.9455 9,501.0
S_Khomani_San-1A + S_Georgian-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Gambian-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Masai-2B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Gambian-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Hungarian-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Mansi-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Iranian-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Bengali-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Iranian-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_BantuKenya-2B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Palestinian-3B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Relli-1A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Bergamo-2A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Somali-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Russian-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Yadava-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_North_Ossetian-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Mala-2A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Adygei-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Khonda_Dora-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Ju_hoan_North-1A Discordant SGDP 109,559,712 – 109,564,735 5,022.5 0.00256954 4 5.4664 14,634.8
S_Khomani_San-1A + S_Kusunda-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + B_Crete-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Brahui-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Yoruba-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Pathan-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + B_Ju_hoan_North-4A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Luo-2A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + B_Yoruba-3A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Sindhi-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Mandenka-1B Discordant SGDP 109,559,712 – 109,568,400 8,688.0 0.00305908 4 7.6175 10,502.1
S_Khomani_San-1A + S_Luo-2B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 8 18.9455 8,445.3
S_Khomani_San-1A + S_Mandenka-2B Discordant SGDP 109,559,712 – 109,564,735 5,022.5 0.00256954 4 5.4664 14,634.8
S_Khomani_San-1A + S_Punjabi-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Mende-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Punjabi-4B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Dinka-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Luhya-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Surui-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Saharawi-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Piapoco-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
S_Khomani_San-1A + S_Estonian-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 4 1.0180 78,587.9
View as figure
Data shown in this table can be downloaded from this page.
α Shape parameter of the Gamma distribution, calculated from the number of pairwise differences along the sequence of the inferred shared haplotype segment (mutation clock), or the breakpoints detected (recombination clock), or both (joint clock); plus the parameter of the coalescent prior distribution (equal to 1 by default).
β Rate parameter of the Gamma distribution, calculated from the physical length of the inferred shared haplotype segment and the mutation rate (mutation clock), or the genetic length given the variable recombination rate (recombination clock), or both (joint clock); plus the parameter of the coalescent prior distribution (equal to 1 by default).
Mean TMRCA Calculated as the mean of the Gamma distribution with parameters α and β, multiplied by 2 x Ne, where Ne = 10,000 by default.
 

The human.genome.dating database is the result of research conducted at the Oxford Big Data Institute at the University of Oxford.

This website was created, designed, and edited by ORCID iD iconPatrick K. Albers

The contents of human.genome.dating are available under the Creative Commons Attribution 4.0 International License (CC BY 4.0) with attribution (citation) required.

human.genome.dating © 2019 - 2025 Contact Terms & Conditions This website does not use cookies and does not collect any personal information about you.