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 Recombination clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP150.1 generations 98  =  1  +  970.990
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_Quechua-1B + S_Tujia-2B Concordant SGDP 135,757,046 – 136,600,964 843,918.5 0.11260757 3 91.0861 658.7
S_Quechua-1B + S_Adygei-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Orcadian-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Tuscan-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + B_Han-3A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 3 138.0456 434.6
S_Tujia-2B + S_Yi-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Ulchi-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Pima-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Cambodian-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Aleut-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Tlingit-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Tubalar-1B Discordant SGDP 136,494,791 – 136,600,964 106,173.0 0.01659883 3 14.2791 4,202.0
S_Quechua-1B + S_Mongola-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Mongola-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Mixtec-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Yemenite_Jew-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + B_Sardinian-3A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Cambodian-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Quechua-3A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Naxi-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Naxi-3A Discordant SGDP 135,477,509 – 136,821,414 1,343,904.5 0.42555128 3 341.4410 175.7
S_Quechua-1B + S_Dai-3B Discordant SGDP 135,760,098 – 136,579,614 819,516.0 0.06749760 3 54.9981 1,090.9
S_Tujia-2B + S_Burmese-2B Discordant SGDP 135,726,038 – 136,821,414 1,095,375.5 0.30881408 3 248.0513 241.9
S_Quechua-1B + S_Miao-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Iranian-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Uygur-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Kyrgyz-2B Discordant SGDP 135,760,098 – 136,600,964 840,866.5 0.07165381 3 58.3230 1,028.8
S_Quechua-1B + S_Xibo-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Lezgin-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Yi-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Spanish-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Mozabite-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + B_Crete-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Dai-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Piapoco-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Xibo-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Mayan-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Quechua-1B + S_Thai-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Yakut-1A Discordant SGDP 136,034,197 – 136,821,414 787,217.0 0.15402219 3 124.2178 483.0
S_Quechua-1B + S_Kinh-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Mansi-1B Discordant SGDP 135,726,038 – 136,643,760 917,722.0 0.21772890 3 175.1831 342.5
S_Quechua-1B + S_Dusun-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Daur-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Chukchi-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Korean-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Mansi-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Dusun-2A Discordant SGDP 135,597,516 – 136,821,414 1,223,898.0 0.32984843 3 264.8787 226.5
S_Quechua-1B + S_Brahmin-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Mozabite-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Burusho-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Samaritan-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Sindhi-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Jordanian-3A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Punjabi-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Norwegian-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Punjabi-4B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Orcadian-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Bulgarian-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_North_Ossetian-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Atayal-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Adygei-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Czech-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Turkish-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_English-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Yemenite_Jew-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_English-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + B_French-3B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_English-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Saharawi-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Estonian-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Piapoco-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Estonian-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Pima-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Finnish-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Mixe-3A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Finnish-3A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Mongola-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Quechua-1B + S_Finnish-3B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Tubalar-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_BantuKenya-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Tlingit-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Saami-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Lahu-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Saami-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Miao-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_French-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Uygur-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Basque-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_She-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Basque-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Korean-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Georgian-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Kinh-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Quechua-1B + S_Greek-2B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + S_Kyrgyz-2A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Quechua-1B + S_Icelandic-1A Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
S_Tujia-2B + B_Mixe-1B Discordant SGDP 135,760,098 – 136,579,614 819,516.0 0.06749760 3 54.9981 1,090.9
S_Quechua-1B + S_Icelandic-1B Discordant SGDP 136,579,496 – 136,579,614 118.0 0.00000406 3 1.0032 59,805.8
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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