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:
X436579517
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 2   position  136,579,517  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 97.7%
2.3%
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 Mutation clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP331.7 generations 98  =  1  +  970.990
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_Quechua-1B + S_Tujia-2B Concordant SGDP 135,757,046 – 136,600,964 843,918.5 0.11260757 6 406.0809 295.5
S_Quechua-1B + S_Adygei-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Orcadian-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Tuscan-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + B_Han-3A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 21 510.4317 822.8
S_Tujia-2B + S_Yi-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Ulchi-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Pima-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Cambodian-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Aleut-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Tlingit-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Tubalar-1B Discordant SGDP 136,494,791 – 136,600,964 106,173.0 0.01659883 7 51.9630 2,694.2
S_Quechua-1B + S_Mongola-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Mongola-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Mixtec-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Yemenite_Jew-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + B_Sardinian-3A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Cambodian-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Quechua-3A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Naxi-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Naxi-3A Discordant SGDP 135,477,509 – 136,821,414 1,343,904.5 0.42555128 20 646.0742 619.1
S_Quechua-1B + S_Dai-3B Discordant SGDP 135,760,098 – 136,579,614 819,516.0 0.06749760 28 394.3677 1,420.0
S_Tujia-2B + S_Burmese-2B Discordant SGDP 135,726,038 – 136,821,414 1,095,375.5 0.30881408 18 526.7802 683.4
S_Quechua-1B + S_Miao-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Iranian-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Uygur-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Kyrgyz-2B Discordant SGDP 135,760,098 – 136,600,964 840,866.5 0.07165381 18 404.6159 889.7
S_Quechua-1B + S_Xibo-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Lezgin-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Yi-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Spanish-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Mozabite-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + B_Crete-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Dai-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Piapoco-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Xibo-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Mayan-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 7 481.9379 290.5
S_Quechua-1B + S_Thai-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Yakut-1A Discordant SGDP 136,034,197 – 136,821,414 787,217.0 0.15402219 12 378.8642 633.5
S_Quechua-1B + S_Kinh-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Mansi-1B Discordant SGDP 135,726,038 – 136,643,760 917,722.0 0.21772890 10 441.5066 453.0
S_Quechua-1B + S_Dusun-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Daur-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Chukchi-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Korean-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Mansi-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Dusun-2A Discordant SGDP 135,597,516 – 136,821,414 1,223,898.0 0.32984843 20 588.4710 679.7
S_Quechua-1B + S_Brahmin-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Mozabite-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Burusho-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Samaritan-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Sindhi-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Jordanian-3A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Punjabi-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Norwegian-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Punjabi-4B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Orcadian-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Bulgarian-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_North_Ossetian-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Atayal-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Adygei-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Czech-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Turkish-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_English-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Yemenite_Jew-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_English-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + B_French-3B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_English-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Saharawi-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Estonian-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Piapoco-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Estonian-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Pima-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Finnish-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Mixe-3A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Finnish-3A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Mongola-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 18 493.3566 729.7
S_Quechua-1B + S_Finnish-3B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Tubalar-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_BantuKenya-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Tlingit-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Saami-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Lahu-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Saami-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Miao-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_French-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Uygur-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Basque-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_She-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Basque-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Korean-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Georgian-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Kinh-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 32 493.3566 1,297.2
S_Quechua-1B + S_Greek-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + S_Kyrgyz-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Quechua-1B + S_Icelandic-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
S_Tujia-2B + B_Mixe-1B Discordant SGDP 135,760,098 – 136,579,614 819,516.0 0.06749760 30 394.3677 1,521.4
S_Quechua-1B + S_Icelandic-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 2 1.0566 37,855.8
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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