HumanGenomeDating
Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
Shared Ancestry Database
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:
X2131670202
Alleles:
reference
T
–
alternate
C
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 10   position  31,670,202  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 95.5%
4.5%
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 Mutation clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP278.1 generations 99  =  1  +  981.000
Pairwise results table Mutation clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Zapotec-1A + S_Zapotec-2A Concordant SGDP 31,445,059 – 31,870,414 425,355.0 0.16889115 3 205.1704 292.4
S_Zapotec-1A + S_Sardinian-1B Discordant SGDP 31,670,199 – 31,827,533 157,334.0 0.00635249 7 76.5203 1,829.6
S_Zapotec-1A + S_Iranian-1B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Saami-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_Russian-2B Discordant SGDP 31,670,199 – 31,792,748 122,548.5 0.00346767 6 59.8233 2,005.9
S_Zapotec-2A + S_Finnish-1A Discordant SGDP 31,583,614 – 31,670,291 86,676.5 0.00250235 4 42.6047 1,877.7
S_Zapotec-2A + S_Papuan-7A Discordant SGDP 31,583,614 – 31,670,291 86,676.5 0.00250235 4 42.6047 1,877.7
S_Zapotec-1A + B_French-3B Discordant SGDP 31,601,307 – 31,670,291 68,984.0 0.00176140 4 34.1123 2,345.2
S_Zapotec-1A + S_Altaian-1B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Yakut-1A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Mongola-2B Discordant SGDP 31,583,614 – 31,670,291 86,676.5 0.00250235 4 42.6047 1,877.7
S_Zapotec-1A + S_Mongola-1A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Quechua-1A Discordant SGDP 31,484,549 – 31,820,336 335,787.0 0.02798754 7 162.1778 863.3
S_Zapotec-1A + S_Mixtec-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Chechen-1B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Turkish-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Even-3A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_Tubalar-1B Discordant SGDP 31,112,961 – 31,670,291 557,329.5 0.27698634 36 268.5182 2,681.4
S_Zapotec-1A + S_Even-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_Kalash-1A Discordant SGDP 31,068,515 – 31,670,291 601,776.0 0.33094296 47 289.8525 3,243.0
S_Zapotec-1A + S_Yakut-2A Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 9 137.6738 1,307.4
S_Zapotec-2A + S_Sardinian-1A Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 40 353.1549 2,265.3
S_Zapotec-1A + S_Aleut-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Mixe-2A Discordant SGDP 31,583,614 – 31,795,978 212,363.5 0.00670084 8 102.9345 1,554.4
S_Zapotec-1A + S_Cambodian-2A Discordant SGDP 31,670,199 – 31,792,748 122,548.5 0.00346767 6 59.8233 2,005.9
S_Zapotec-1A + S_Basque-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Naxi-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Druze-2A Discordant SGDP 31,670,199 – 31,792,748 122,548.5 0.00346767 6 59.8233 2,005.9
S_Zapotec-1A + S_Naxi-3B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Kyrgyz-2B Discordant SGDP 31,628,003 – 31,670,291 42,287.5 0.00098154 2 21.2980 1,878.1
S_Zapotec-1A + S_Tu-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Adygei-2A Discordant SGDP 31,583,614 – 31,824,938 241,323.5 0.00807858 8 116.8353 1,369.4
S_Zapotec-1A + S_Oroqen-1A Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 15 353.1549 849.5
S_Zapotec-1A + S_Yemenite_Jew-2A Discordant SGDP 31,670,199 – 32,451,906 781,706.5 0.48735274 110 376.2191 5,847.7
S_Zapotec-1A + S_Daur-2A Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 9 353.1549 509.7
S_Zapotec-2A + S_Mixtec-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 5 154.7210 646.3
S_Zapotec-1A + S_Hezhen-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_Papuan-4B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_She-1A Discordant SGDP 31,134,695 – 31,670,291 535,595.5 0.24096685 61 258.0858 4,727.1
S_Zapotec-2A + S_Papuan-9A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Korean-2B Discordant SGDP 31,134,695 – 31,827,533 692,838.0 0.24731908 23 333.5622 1,379.1
S_Zapotec-2A + S_English-1B Discordant SGDP 31,134,695 – 31,983,119 848,423.5 0.50274832 38 408.2433 1,861.6
S_Zapotec-1A + S_Burmese-2B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_Greek-1B Discordant SGDP 31,630,936 – 31,670,291 39,354.5 0.00088213 2 19.8902 2,011.0
S_Zapotec-1A + S_Burmese-1A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_Orcadian-1A Discordant SGDP 31,628,003 – 31,670,291 42,287.5 0.00098154 2 21.2980 1,878.1
S_Zapotec-1A + S_Thai-1A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_Spanish-2B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Thai-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Saami-1B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + B_Australian-3A Discordant SGDP 31,583,614 – 31,670,291 86,676.5 0.00250235 4 42.6047 1,877.7
S_Zapotec-1A + S_Basque-1B Discordant SGDP 31,670,199 – 31,792,748 122,548.5 0.00346767 6 59.8233 2,005.9
S_Zapotec-1A + B_Australian-4B Discordant SGDP 31,583,614 – 31,670,291 86,676.5 0.00250235 4 42.6047 1,877.7
S_Zapotec-1A + S_Icelandic-1A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Papuan-3A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Iranian-2B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Papuan-1A Discordant SGDP 31,583,614 – 31,670,291 86,676.5 0.00250235 4 42.6047 1,877.7
S_Zapotec-1A + S_BedouinB-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Papuan-8A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Tuscan-2B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 9 137.6738 1,307.4
S_Zapotec-1A + S_Igorot-1A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Orcadian-2B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Chukchi-1B Discordant SGDP 31,583,614 – 31,670,291 86,676.5 0.00250235 3 42.6047 1,408.3
S_Zapotec-1A + S_Lezgin-2A Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 10 137.6738 1,452.7
S_Zapotec-1A + S_Itelman-1B Discordant SGDP 31,496,660 – 31,868,351 371,691.0 0.03014480 8 179.4117 891.8
S_Zapotec-1A + S_Tajik-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Eskimo_Naukan-1A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Turkish-1A Discordant SGDP 31,670,199 – 32,451,906 781,706.5 0.48735274 110 376.2191 5,847.7
S_Zapotec-1A + S_Kapu-1A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Yemenite_Jew-1B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Irula-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Pima-2B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Mala-3A Discordant SGDP 31,134,695 – 31,670,291 535,595.5 0.24096685 34 258.0858 2,634.8
S_Zapotec-2A + S_Quechua-1B Discordant SGDP 31,583,614 – 31,841,841 258,227.0 0.00989188 12 124.9490 1,920.8
S_Zapotec-1A + S_Brahmin-1B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_Maori-1B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Kusunda-1B Discordant SGDP 31,134,695 – 31,670,291 535,595.5 0.24096685 22 258.0858 1,704.9
S_Zapotec-2A + S_Papuan-14A Discordant SGDP 31,112,961 – 31,670,291 557,329.5 0.27698634 43 268.5182 3,202.8
S_Zapotec-1A + S_Brahui-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_Papuan-7B Discordant SGDP 31,583,614 – 31,670,291 86,676.5 0.00250235 4 42.6047 1,877.7
S_Zapotec-1A + S_Makrani-1A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_Mansi-2A Discordant SGDP 31,134,695 – 31,670,291 535,595.5 0.24096685 15 258.0858 1,162.4
S_Zapotec-1A + S_Brahui-1B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_English-1A Discordant SGDP 31,134,695 – 31,727,319 592,624.0 0.24244048 20 285.4595 1,401.2
S_Zapotec-1A + S_Burusho-1A Discordant SGDP 31,620,012 – 31,670,291 50,279.0 0.00121443 2 25.1339 1,591.5
S_Zapotec-2A + S_Estonian-2B Discordant SGDP 31,134,695 – 31,670,291 535,595.5 0.24096685 19 258.0858 1,472.4
S_Zapotec-1A + S_Kalash-1B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_French-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Burusho-2A Discordant SGDP 31,670,199 – 31,827,533 157,334.0 0.00635249 7 76.5203 1,829.6
S_Zapotec-2A + S_Hungarian-2B Discordant SGDP 31,620,012 – 31,670,291 50,279.0 0.00121443 2 25.1339 1,591.5
S_Zapotec-1A + S_Hazara-1A Discordant SGDP 31,636,829 – 31,670,291 33,461.5 0.00067196 2 17.0615 2,344.5
S_Zapotec-2A + S_Kyrgyz-1B Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Sindhi-2B Discordant SGDP 31,583,614 – 31,670,291 86,676.5 0.00250235 4 42.6047 1,877.7
S_Zapotec-2A + S_Polish-1A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-1A + S_Punjabi-3A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
S_Zapotec-2A + S_North_Ossetian-2A Discordant SGDP 31,134,695 – 31,670,291 535,595.5 0.24096685 24 258.0858 1,859.8
S_Zapotec-1A + S_Armenian-1A Discordant SGDP 31,670,199 – 31,868,351 198,152.0 0.00956847 9 96.1130 1,872.8
S_Zapotec-2A + S_Chane-1A Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 19 353.1549 1,076.0
S_Zapotec-1A + S_Czech-2A Discordant SGDP 31,670,199 – 31,670,291 91.5 0.00000026 2 1.0439 38,317.1
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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