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:
X436525854
Alleles:
reference
C
–
alternate
A
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 2   position  136,525,854  (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 Recombination clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP227.6 generations 98  =  1  +  971.000
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_Ju_hoan_North-3B + S_Ju_hoan_North-2A Concordant SGDP 136,411,978 – 137,134,850 722,872.5 0.65142718 3 522.1417 114.9
S_Ju_hoan_North-2A + S_Irula-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Mozabite-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Eskimo_Chaplin-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Karitiana-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Tajik-2A Discordant SGDP 136,494,791 – 136,739,216 244,424.5 0.03228080 3 26.8246 2,236.7
S_Ju_hoan_North-2A + S_Icelandic-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_English-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Xibo-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Oroqen-2A Discordant SGDP 136,493,766 – 136,739,216 245,450.0 0.03252613 3 27.0209 2,220.5
S_Ju_hoan_North-3B + S_Mansi-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Tlingit-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Eskimo_Chaplin-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Even-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Aleut-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Brahui-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Abkhasian-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Yi-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Finnish-3B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Chukchi-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Jordanian-3A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Itelman-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + B_Dai-4A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 3 27.9656 2,145.5
S_Ju_hoan_North-3B + S_Eskimo_Naukan-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Ulchi-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Somali-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Even-1B Discordant SGDP 136,525,764 – 136,762,052 236,287.5 0.02966598 3 24.7328 2,425.9
S_Ju_hoan_North-3B + S_Makrani-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Kinh-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Burusho-1B Discordant SGDP 135,759,069 – 136,762,052 1,002,983.0 0.09320676 3 75.5654 794.0
S_Ju_hoan_North-2A + S_Pathan-1B Discordant SGDP 136,476,284 – 136,762,052 285,767.5 0.03668983 3 30.3519 1,976.8
S_Ju_hoan_North-3B + S_Burusho-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Punjabi-3B Discordant SGDP 136,493,766 – 136,750,428 256,662.0 0.03265136 3 27.1211 2,212.3
S_Ju_hoan_North-3B + S_Hazara-1A Discordant SGDP 136,494,791 – 136,554,977 60,185.5 0.00716495 3 6.7320 8,912.7
S_Ju_hoan_North-2A + S_Atayal-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Sindhi-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Estonian-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Punjabi-2A Discordant SGDP 136,493,766 – 136,739,216 245,450.0 0.03252613 3 27.0209 2,220.5
S_Ju_hoan_North-2A + S_Basque-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Bulgarian-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Sardinian-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Bulgarian-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Adygei-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Bulgarian-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Yemenite_Jew-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_English-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + B_Sardinian-3A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_English-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_BantuHerero-1B Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 3 27.9656 2,145.5
S_Ju_hoan_North-3B + S_Estonian-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Eskimo_Sireniki-1B Discordant SGDP 136,525,764 – 136,762,052 236,287.5 0.02966598 3 24.7328 2,425.9
S_Ju_hoan_North-3B + S_Finnish-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Aleut-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Finnish-3A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Oroqen-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_BantuKenya-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Uygur-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_French-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Eskimo_Sireniki-2A Discordant SGDP 136,476,284 – 136,762,052 285,767.5 0.03668983 3 30.3519 1,976.8
S_Ju_hoan_North-3B + S_French-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Brahmin-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Basque-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Balochi-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Georgian-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Burusho-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Greek-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Punjabi-4B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Icelandic-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Albanian-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Iranian-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_English-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Palestinian-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Estonian-2A Discordant SGDP 136,476,284 – 136,677,400 201,116.0 0.03439504 3 28.5160 2,104.1
S_Ju_hoan_North-3B + S_Tuscan-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Estonian-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Norwegian-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Saami-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Orcadian-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Hungarian-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Orcadian-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Bergamo-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_North_Ossetian-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Tuscan-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Spanish-1B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Orcadian-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Spanish-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Spanish-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Tajik-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Yemenite_Jew-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + B_Karitiana-3B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + B_Crete-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-3B + S_Saharawi-2A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + B_Papuan-15A Discordant SGDP 136,493,766 – 136,750,428 256,662.0 0.03265136 3 27.1211 2,212.3
S_Ju_hoan_North-2A + S_Mozabite-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Chane-1A Discordant SGDP 136,493,766 – 136,750,428 256,662.0 0.03265136 3 27.1211 2,212.3
S_Ju_hoan_North-2A + S_Mixe-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Pima-1A Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
S_Ju_hoan_North-2A + S_Mongola-2B Discordant SGDP 136,525,764 – 136,525,855 91.0 0.00000687 3 1.0055 59,671.8
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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