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

rs545477317
Alleles:
reference
G
ancestral
alternate
C
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 2   position  136,642,417  (GRCh37) Explore rs545477317 on Ensembl!
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 Joint clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP407.6 generations 99  =  1  +  981.000
Pairwise results table Joint clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Mbuti-2A + S_Mbuti-2B Concordant SGDP 136,389,477 – 137,436,119 1,046,642.0 0.92134495 7 1,240.4641 112.9
S_Mbuti-2B + S_Brahmin-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Kinh-2B Discordant SGDP 136,639,066 – 136,642,425 3,359.0 0.00072107 4 3.1892 25,084.8
S_Mbuti-2B + S_Oroqen-2B Discordant SGDP 136,599,475 – 136,642,425 42,950.5 0.00851458 8 28.4279 5,628.3
S_Mbuti-2B + S_BantuHerero-2B Discordant SGDP 135,760,098 – 136,642,425 882,327.5 0.07991711 246 488.4509 10,072.7
S_Mbuti-2B + S_Adygei-1B Discordant SGDP 135,760,098 – 136,642,425 882,327.5 0.07991711 258 488.4509 10,564.0
S_Mbuti-2B + S_Bergamo-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Estonian-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Dai-3A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Naxi-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Cambodian-1B Discordant SGDP 136,619,416 – 136,642,425 23,009.5 0.00537376 6 16.3436 7,342.3
S_Mbuti-2A + S_Aleut-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Mongola-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Mixtec-2B Discordant SGDP 136,602,042 – 136,642,425 40,383.5 0.00808140 7 26.8492 5,214.3
S_Mbuti-2B + S_Sindhi-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Czech-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Oroqen-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Saami-1A Discordant SGDP 136,602,042 – 136,642,425 40,383.5 0.00808140 10 26.8492 7,449.0
S_Mbuti-2A + S_Uygur-1B Discordant SGDP 136,639,066 – 136,642,425 3,359.0 0.00072107 4 3.1892 25,084.8
S_Mbuti-2B + S_Lezgin-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Xibo-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + B_Crete-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Yi-2B Discordant SGDP 136,639,066 – 136,642,425 3,359.0 0.00072107 4 3.1892 25,084.8
S_Mbuti-2A + S_Mozabite-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Mozabite-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Xibo-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Eskimo_Naukan-2A Discordant SGDP 136,599,475 – 136,642,425 42,950.5 0.00851458 7 28.4279 4,924.7
S_Mbuti-2B + S_Dusun-2A Discordant SGDP 136,639,066 – 136,642,425 3,359.0 0.00072107 4 3.1892 25,084.8
S_Mbuti-2A + S_Mansi-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Burusho-1A Discordant SGDP 136,619,416 – 136,642,425 23,009.5 0.00537376 7 16.3436 8,566.1
S_Mbuti-2A + S_Madiga-1A Discordant SGDP 136,619,416 – 136,642,425 23,009.5 0.00537376 6 16.3436 7,342.3
S_Mbuti-2B + S_Bulgarian-1B Discordant SGDP 136,602,042 – 136,642,425 40,383.5 0.00808140 8 26.8492 5,959.2
S_Mbuti-2A + S_Balochi-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_BantuKenya-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Brahui-1B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Finnish-1B Discordant SGDP 136,602,042 – 136,642,425 40,383.5 0.00808140 8 26.8492 5,959.2
S_Mbuti-2A + S_Burusho-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Hungarian-2B Discordant SGDP 136,619,416 – 136,642,425 23,009.5 0.00537376 8 16.3436 9,789.8
S_Mbuti-2A + S_Punjabi-3B Discordant SGDP 136,619,416 – 136,642,425 23,009.5 0.00537376 6 16.3436 7,342.3
S_Mbuti-2B + S_Orcadian-2A Discordant SGDP 136,602,042 – 136,642,425 40,383.5 0.00808140 8 26.8492 5,959.2
S_Mbuti-2A + S_Punjabi-4B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_North_Ossetian-1A Discordant SGDP 136,619,416 – 136,642,425 23,009.5 0.00537376 7 16.3436 8,566.1
S_Mbuti-2A + S_Atayal-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Spanish-1B Discordant SGDP 136,602,042 – 136,642,425 40,383.5 0.00808140 8 26.8492 5,959.2
S_Mbuti-2A + S_English-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Saharawi-2A Discordant SGDP 136,619,416 – 136,642,425 23,009.5 0.00537376 8 16.3436 9,789.8
S_Mbuti-2A + S_English-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Pima-1B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_English-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Miao-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Saami-2B Discordant SGDP 136,602,042 – 136,642,425 40,383.5 0.00808140 8 26.8492 5,959.2
S_Mbuti-2B + S_Hezhen-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Basque-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Dai-1A Discordant SGDP 135,760,098 – 136,642,425 882,327.5 0.07991711 258 488.4509 10,564.0
S_Mbuti-2A + S_Basque-1B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Kinh-1A Discordant SGDP 135,760,098 – 136,642,425 882,327.5 0.07991711 248 488.4509 10,154.6
S_Mbuti-2A + S_Georgian-1B Discordant SGDP 136,619,416 – 136,642,425 23,009.5 0.00537376 6 16.3436 7,342.3
S_Mbuti-2B + S_Chukchi-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Greek-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Kusunda-2B Discordant SGDP 135,760,098 – 136,642,425 882,327.5 0.07991711 244 488.4509 9,990.8
S_Mbuti-2A + S_Icelandic-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Hazara-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Iranian-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Punjabi-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Tuscan-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Bulgarian-2B Discordant SGDP 135,760,098 – 136,642,425 882,327.5 0.07991711 257 488.4509 10,523.1
S_Mbuti-2A + S_Jordanian-3A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_English-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Norwegian-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Estonian-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Norwegian-1B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Estonian-1B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Orcadian-1B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Finnish-3B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Adygei-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_French-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Spanish-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Icelandic-1B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Tajik-2A Discordant SGDP 136,619,416 – 136,642,425 23,009.5 0.00537376 6 16.3436 7,342.3
S_Mbuti-2B + S_Kyrgyz-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Tajik-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Polish-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Turkish-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Lezgin-1B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Yemenite_Jew-1B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_North_Ossetian-2A Discordant SGDP 136,639,066 – 136,642,425 3,359.0 0.00072107 4 3.1892 25,084.8
S_Mbuti-2A + B_French-3A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Adygei-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2A + S_Mandenka-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Yemenite_Jew-2B Discordant SGDP 136,619,416 – 136,642,425 23,009.5 0.00537376 7 16.3436 8,566.1
S_Mbuti-2A + S_Karitiana-1B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + B_French-3A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Mixe-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Chane-1B Discordant SGDP 136,602,042 – 136,642,425 40,383.5 0.00808140 8 26.8492 5,959.2
S_Mbuti-2B + S_Mongola-2B Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Piapoco-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Tubalar-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Pima-2A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
S_Mbuti-2B + S_Tlingit-1A Discordant SGDP 136,642,417 – 136,642,425 8.5 0.00000187 4 1.0056 79,556.7
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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