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Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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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

rs376354757
Alleles:
reference
A
ancestral
alternate
T
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  31,673,976  (GRCh37) Explore rs376354757 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.5%
0.5%
AFR 96.6%
3.4%
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 Recombination clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP10,810.9 generations 98  =  3  +  951.000
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_Mbuti-3A + S_Mbuti-2B Concordant SGDP 31,556,725 – 31,702,925 146,200.5 0.00729163 3 6.8333 8,780.5
S_Biaka-2A + S_Mbuti-2B Concordant SGDP 31,645,663 – 31,820,336 174,673.5 0.00539778 3 5.3182 11,282.0
S_Biaka-2A + S_Mbuti-3A Concordant SGDP 31,636,346 – 31,674,085 37,738.5 0.00073106 3 1.5848 37,858.5
S_Biaka-2A + S_Jordanian-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Polish-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Mongola-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Sardinian-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Han-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Kalash-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_BantuTswana-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + B_Sardinian-3B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Even-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Yakut-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Even-3B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Ulchi-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Tubalar-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Lezgin-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Tujia-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Yemenite_Jew-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Hezhen-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-3A + S_Miao-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_She-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Bougainville-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Tu-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Yemenite_Jew-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Korean-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Bergamo-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Thai-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Tuscan-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + B_Australian-4A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Kyrgyz-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Maori-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Chechen-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Maori-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Turkish-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Papuan-3B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + B_Han-3A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Bougainville-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Piapoco-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Papuan-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-3A + S_Thai-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Papuan-5B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + B_Australian-3B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Papuan-4B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Madiga-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Icelandic-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Saami-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Druze-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Papuan-14A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Mozabite-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Iranian-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Papuan-7B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_BedouinB-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Papuan-9B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Sardinian-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Papuan-12B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Sardinian-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Papuan-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Jordanian-3B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Chukchi-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Kyrgyz-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Mansi-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Orcadian-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Irula-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Russian-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Khonda_Dora-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Saharawi-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Brahmin-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Spanish-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Brahui-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Yemenite_Jew-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Brahui-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + B_French-3B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Kalash-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + B_Papuan-15A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Burusho-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + B_Dinka-3B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Abkhasian-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Pima-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Bulgarian-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-3A + S_Oroqen-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Czech-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Tubalar-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Estonian-2A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Oroqen-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Estonian-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Dusun-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Finnish-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Mala-3B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_French-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Makrani-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_French-2B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Armenian-1B Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Georgian-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + S_Iranian-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Greek-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Mbuti-2B + B_French-3A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
S_Biaka-2A + S_Icelandic-1A Discordant SGDP 31,673,934 – 31,674,085 151.0 0.00000047 3 1.0004 59,977.4
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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