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Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
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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

rs12257591
Alleles:
reference
G
ancestral
alternate
A
derived
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
How was the ancestral/derived state determined?Chromosome 10   position  31,822,106  (GRCh37) Explore rs12257591 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.4%
1.6%
AFR 90.9%
9.1%
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 99.3%
0.7%
reference ← allele frequency → alternate
Select clock model
  Mutation clock
  Recombination clock
  Joint clock
Age estimation summary Recombination clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP25,488.8 generations 136  =  36  +  1000.694
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_Saharawi-2A + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Saharawi-2A + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 1.1372 52,763.4
S_Saharawi-2A + S_Esan-1B Concordant SGDP 31,819,482 – 31,824,938 5,456.0 0.00074315 3 1.5945 37,628.8
S_Esan-1B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Saharawi-2A + S_Luhya-2B Concordant SGDP 31,819,482 – 31,824,938 5,456.0 0.00074315 3 1.5945 37,628.8
S_Yoruba-2B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 1.1372 52,763.4
S_Luhya-2B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 1.1372 52,763.4
S_Luhya-2B + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 1.1372 52,763.4
S_Biaka-2A + S_Esan-2B Concordant SGDP 31,822,100 – 31,841,841 19,741.5 0.00198474 3 2.5878 23,185.8
S_Biaka-2A + S_Khomani_San-2B Concordant SGDP 31,693,149 – 31,822,112 128,963.0 0.00457854 3 4.6628 12,867.7
S_Biaka-2A + S_Esan-1B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Biaka-2A + S_Yoruba-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 1.1372 52,763.4
S_Biaka-2A + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-2B + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 1.1372 52,763.4
S_Luhya-2B + S_Yoruba-2B Concordant SGDP 31,688,920 – 31,827,533 138,613.5 0.00557346 3 5.4588 10,991.5
S_Khomani_San-2B + S_Georgian-2B Concordant SGDP 31,822,025 – 31,822,112 87.0 0.00000145 3 1.0012 59,930.2
S_Luhya-2B + S_Esan-1B Concordant SGDP 31,688,920 – 31,827,533 138,613.5 0.00557346 3 5.4588 10,991.5
S_Esan-1B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Luhya-2B + S_Esan-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 1.1372 52,763.4
S_Esan-1B + S_Esan-2B Concordant SGDP 31,819,482 – 31,824,938 5,456.0 0.00074315 3 1.5945 37,628.8
S_Luhya-2B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 1.1372 52,763.4
S_Saharawi-2A + S_Biaka-2A Concordant SGDP 31,820,336 – 31,841,841 21,505.0 0.00222725 3 2.7818 21,568.8
S_Georgian-2B + B_Mbuti-4A Concordant SGDP 31,821,907 – 31,822,112 204.5 0.00000342 3 1.0027 59,836.3
S_Saharawi-2A + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Saharawi-2A + S_Yoruba-2B Concordant SGDP 31,819,482 – 31,822,112 2,630.0 0.00057191 3 1.4575 41,165.5
S_Yoruba-2B + B_Mbuti-4A Concordant SGDP 31,822,100 – 32,051,343 229,243.0 0.33866899 3 271.9352 220.6
S_Saharawi-2A + S_Esan-2B Concordant SGDP 31,614,944 – 31,965,047 350,103.0 0.24796352 3 199.3708 300.9
S_Yoruba-2B + S_Esan-1B Concordant SGDP 31,536,157 – 31,874,064 337,906.5 0.12244606 3 98.9568 606.3
S_Esan-2B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Esan-2B Concordant SGDP 31,819,482 – 31,822,112 2,630.0 0.00057191 3 1.4575 41,165.5
S_Esan-2B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Khomani_San-2B + B_Mbuti-4A Concordant SGDP 31,485,956 – 31,824,938 338,982.0 0.02792865 3 23.3429 2,570.4
S_Biaka-2A + S_Luhya-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 1.1372 52,763.4
S_Biaka-2A + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_North_Ossetian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Jordanian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Palestinian-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Icelandic-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Estonian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Punjabi-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Czech-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Sardinian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Palestinian-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Icelandic-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Georgian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_French-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Estonian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Chane-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Jordanian-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Orcadian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Brahmin-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Spanish-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Albanian-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + B_Sardinian-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Finnish-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Zapotec-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Iraqi_Jew-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Quechua-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Bergamo-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Even-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Orcadian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Aleut-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + B_French-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Burmese-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Piapoco-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Papuan-4A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Abkhasian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Bulgarian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Atayal-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Biaka-2A + S_Polish-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_English-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Georgian-2B + S_Saharawi-2B Discordant SGDP 31,484,549 – 31,841,841 357,292.0 0.03021478 3 25.1718 2,383.6
S_Yoruba-2B + S_Saami-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Tubalar-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Georgian-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Yakut-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Greek-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Tu-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Iraqi_Jew-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Uygur-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Bergamo-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_She-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Tuscan-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Korean-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Kyrgyz-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Thai-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Chechen-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Maori-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Turkish-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Maori-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Pima-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Bougainville-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Mixtec-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Papuan-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Ulchi-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Papuan-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_BantuTswana-1B Discordant SGDP 31,536,157 – 32,453,323 917,166.0 0.54162157 3 434.2973 138.2
S_Yoruba-2B + S_Papuan-10B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Burmese-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Papuan-4A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Bougainville-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Papuan-14A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Mala-3A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Papuan-7A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Madiga-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Papuan-7B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Luhya-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Papuan-9B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Albanian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Papuan-12A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Finnish-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Papuan-12B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Basque-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Chukchi-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Iraqi_Jew-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Mansi-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Samaritan-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Bengali-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Bergamo-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Kapu-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Sardinian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Relli-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Jordanian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Irula-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Lezgin-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Mala-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Turkish-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Pathan-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + B_Papuan-15B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Hazara-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Esan-1B + S_Karitiana-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Kalash-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Saharawi-2A + S_Mende-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
S_Yoruba-2B + S_Kalash-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0002 59,990.4
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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