HumanGenomeDating
Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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TGP
1000 Genomes Project
Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
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SGDP
Simons Genome Diversity Project
Populations: 130
Individuals: 278
Ancestry analyses:6,800,992
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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:
X2131612296
Alleles:
reference
A
–
alternate
G
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 10   position  31,612,296  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 98.7%
1.3%
AFR 93.2%
6.8%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 98.9%
1.1%
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 Recombination clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP22,376.2 generations 116  =  17  +  990.960
Pairwise results table Recombination clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_BantuHerero-2B + S_Ju_hoan_North-2A Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 3 1.6157 37,136.4
S_BantuHerero-2B + S_Ju_hoan_North-2B Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 3 1.6157 37,136.4
S_BantuHerero-2B + S_Hezhen-1B Concordant SGDP 31,601,307 – 31,630,246 28,939.5 0.00085186 3 1.6815 35,682.7
S_BantuHerero-2B + S_Masai-1A Concordant SGDP 31,548,330 – 31,870,414 322,084.0 0.04569690 3 37.5575 1,597.5
S_Ju_hoan_North-1B + S_Hezhen-1B Concordant SGDP 31,611,088 – 31,612,415 1,326.5 0.00003844 3 1.0308 58,209.9
S_Ju_hoan_North-1B + B_Ju_hoan_North-4B Concordant SGDP 31,068,515 – 31,870,414 801,899.0 0.36691039 3 294.5283 203.7
S_Ju_hoan_North-2B + S_Ju_hoan_North-1B Concordant SGDP 31,556,603 – 31,870,414 313,810.5 0.04203703 3 34.6296 1,732.6
S_Ju_hoan_North-2B + B_Ju_hoan_North-4B Concordant SGDP 31,556,603 – 31,873,306 316,702.5 0.10924376 3 88.3950 678.8
S_Ju_hoan_North-2B + S_Hezhen-1B Concordant SGDP 31,611,088 – 31,612,415 1,326.5 0.00003844 3 1.0308 58,209.9
S_Ju_hoan_North-2B + S_Masai-1A Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 3 1.6157 37,136.4
S_Ju_hoan_North-2A + S_Masai-1A Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 3 1.6157 37,136.4
S_Masai-1A + B_Ju_hoan_North-4B Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 3 1.6157 37,136.4
S_Masai-1A + S_Ju_hoan_North-1B Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 3 1.6157 37,136.4
S_BantuHerero-2B + S_Ju_hoan_North-1B Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 3 1.6157 37,136.4
S_BantuHerero-2B + B_Ju_hoan_North-4B Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 3 1.6157 37,136.4
S_Hezhen-1B + B_Ju_hoan_North-4B Concordant SGDP 31,611,088 – 31,612,415 1,326.5 0.00003844 3 1.0308 58,209.9
S_Masai-1A + S_Hezhen-1B Concordant SGDP 31,601,307 – 31,628,577 27,270.0 0.00079667 3 1.6373 36,644.8
S_Masai-1A + S_Saharawi-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Abkhasian-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Tuscan-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Karitiana-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Ami-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Mala-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Yemenite_Jew-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Yi-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Daur-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Sindhi-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + B_French-3B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Russian-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Kyrgyz-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Hungarian-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Finnish-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Greek-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Hezhen-1B + S_Oroqen-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Jordanian-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Hezhen-1B + S_Xibo-1B Discordant SGDP 31,545,842 – 31,727,319 181,477.0 0.01596109 3 13.7689 4,357.7
S_Masai-1A + S_Orcadian-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Mongola-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Tajik-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Tubalar-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Zapotec-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Yakut-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Burmese-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Altaian-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Iranian-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Even-3B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_BantuTswana-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Even-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Uygur-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Yakut-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Kinh-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Even-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Czech-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Cambodian-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Yemenite_Jew-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Han-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_BantuHerero-2B + S_Luhya-1B Discordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 3 1.6157 37,136.4
S_Masai-1A + S_Oroqen-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Sindhi-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Uygur-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Czech-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Yi-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Estonian-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Yi-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Saami-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Dai-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Masai-2B Discordant SGDP 31,556,184 – 31,752,325 196,140.5 0.00855601 3 7.8448 7,648.4
S_Masai-1A + S_She-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Tuscan-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_She-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Kyrgyz-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Tu-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Orcadian-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Korean-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Russian-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Ami-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Spanish-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Thai-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + B_Dai-4B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Thai-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Piapoco-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Dusun-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Quechua-3A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Maori-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Korean-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Papuan-3B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Hazara-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Papuan-5B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Georgian-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Papuan-9B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2A + S_Sardinian-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Papuan-12B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Mixtec-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Papuan-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Naxi-3A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Eskimo_Sireniki-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Tujia-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Bengali-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Naxi-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Irula-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Thai-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Mala-3A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Hawaiian-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Madiga-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Sindhi-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Kusunda-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Icelandic-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Kusunda-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Abkhasian-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Kusunda-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Ju_hoan_North-2B + S_Khomani_San-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Balochi-1B Discordant SGDP 31,556,184 – 31,868,351 312,167.0 0.01573451 3 13.5876 4,415.8
S_BantuHerero-2B + S_Mozabite-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Brahui-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_BantuHerero-2B + S_Dinka-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
S_Masai-1A + S_Kalash-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 3 1.0011 59,931.4
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.
 

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