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 Joint clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP20,093.8 generations 116  =  17  +  990.960
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_BantuHerero-2B + S_Ju_hoan_North-2A Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 5 13.4145 7,454.6
S_BantuHerero-2B + S_Ju_hoan_North-2B Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 7 13.4145 10,436.4
S_BantuHerero-2B + S_Hezhen-1B Concordant SGDP 31,601,307 – 31,630,246 28,939.5 0.00085186 4 15.5724 5,137.3
S_BantuHerero-2B + S_Masai-1A Concordant SGDP 31,548,330 – 31,870,414 322,084.0 0.04569690 17 192.1578 1,769.4
S_Ju_hoan_North-1B + S_Hezhen-1B Concordant SGDP 31,611,088 – 31,612,415 1,326.5 0.00003844 3 1.6675 35,982.6
S_Ju_hoan_North-1B + B_Ju_hoan_North-4B Concordant SGDP 31,068,515 – 31,870,414 801,899.0 0.36691039 35 679.4398 1,030.3
S_Ju_hoan_North-2B + S_Ju_hoan_North-1B Concordant SGDP 31,556,603 – 31,870,414 313,810.5 0.04203703 20 185.2587 2,159.1
S_Ju_hoan_North-2B + B_Ju_hoan_North-4B Concordant SGDP 31,556,603 – 31,873,306 316,702.5 0.10924376 26 240.4122 2,163.0
S_Ju_hoan_North-2B + S_Hezhen-1B Concordant SGDP 31,611,088 – 31,612,415 1,326.5 0.00003844 3 1.6675 35,982.6
S_Ju_hoan_North-2B + S_Masai-1A Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 8 13.4145 11,927.4
S_Ju_hoan_North-2A + S_Masai-1A Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 6 13.4145 8,945.5
S_Masai-1A + B_Ju_hoan_North-4B Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 7 13.4145 10,436.4
S_Masai-1A + S_Ju_hoan_North-1B Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 6 13.4145 8,945.5
S_BantuHerero-2B + S_Ju_hoan_North-1B Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 5 13.4145 7,454.6
S_BantuHerero-2B + B_Ju_hoan_North-4B Concordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 6 13.4145 8,945.5
S_Hezhen-1B + B_Ju_hoan_North-4B Concordant SGDP 31,611,088 – 31,612,415 1,326.5 0.00003844 3 1.6675 35,982.6
S_Masai-1A + S_Hezhen-1B Concordant SGDP 31,601,307 – 31,628,577 27,270.0 0.00079667 4 14.7269 5,432.2
S_Masai-1A + S_Saharawi-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Abkhasian-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Tuscan-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Karitiana-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Ami-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Mala-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Yemenite_Jew-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Yi-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Daur-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Sindhi-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + B_French-3B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Russian-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Kyrgyz-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Hungarian-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Finnish-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Greek-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Hezhen-1B + S_Oroqen-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Jordanian-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Hezhen-1B + S_Xibo-1B Discordant SGDP 31,545,842 – 31,727,319 181,477.0 0.01596109 10 100.8778 1,982.6
S_Masai-1A + S_Orcadian-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Mongola-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Tajik-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Tubalar-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Zapotec-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Yakut-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Burmese-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Altaian-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Iranian-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Even-3B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_BantuTswana-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Even-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Uygur-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Yakut-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Kinh-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Even-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Czech-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Cambodian-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Yemenite_Jew-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Han-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_BantuHerero-2B + S_Luhya-1B Discordant SGDP 31,612,248 – 31,636,829 24,581.0 0.00076958 8 13.4145 11,927.4
S_Masai-1A + S_Oroqen-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Sindhi-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Uygur-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Czech-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Yi-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Estonian-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Yi-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Saami-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Dai-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Masai-2B Discordant SGDP 31,556,184 – 31,752,325 196,140.5 0.00855601 23 101.9922 4,510.1
S_Masai-1A + S_She-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Tuscan-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_She-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Kyrgyz-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Tu-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Orcadian-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Korean-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Russian-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Ami-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Spanish-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Thai-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + B_Dai-4B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Thai-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Piapoco-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Dusun-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Quechua-3A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Maori-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Korean-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Papuan-3B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Hazara-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Papuan-5B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Georgian-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Papuan-9B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2A + S_Sardinian-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Papuan-12B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Mixtec-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Papuan-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Naxi-3A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Eskimo_Sireniki-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Tujia-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Bengali-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Naxi-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Irula-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Thai-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Mala-3A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Hawaiian-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Madiga-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Sindhi-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Kusunda-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Icelandic-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Kusunda-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Abkhasian-2A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Kusunda-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Ju_hoan_North-2B + S_Khomani_San-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Balochi-1B Discordant SGDP 31,556,184 – 31,868,351 312,167.0 0.01573451 27 163.4278 3,304.2
S_BantuHerero-2B + S_Mozabite-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Brahui-1A Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_BantuHerero-2B + S_Dinka-1B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
S_Masai-1A + S_Kalash-2B Discordant SGDP 31,612,248 – 31,612,297 48.5 0.00000143 4 1.0244 78,092.7
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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