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Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
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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

rs111646552
Alleles:
reference
G
ancestral
alternate
A
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  136,545,770  (GRCh37) Explore rs111646552 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 A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP1,289.4 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_Khomani_San-2A + S_Khomani_San-2B Concordant SGDP 135,755,745 – 136,781,557 1,025,812.0 0.16248506 20 623.3778 641.7
S_Khomani_San-2B + S_Dusun-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Oroqen-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Eskimo_Chaplin-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Chane-1A Discordant SGDP 136,545,769 – 136,735,800 190,031.0 0.02656575 22 113.4675 3,877.8
S_Khomani_San-2B + S_Adygei-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Basque-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Atayal-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Aleut-2A Discordant SGDP 136,545,769 – 136,735,800 190,031.0 0.02656575 31 113.4675 5,464.1
S_Khomani_San-2A + S_Even-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Tubalar-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Mongola-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Mongola-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Mixtec-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Madiga-1B Discordant SGDP 136,545,769 – 136,735,800 190,031.0 0.02656575 26 113.4675 4,582.8
S_Khomani_San-2B + S_Sindhi-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Cambodian-1B Discordant SGDP 136,545,769 – 136,714,614 168,845.0 0.02634980 29 103.1254 5,624.2
S_Khomani_San-2B + S_Finnish-3B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Oroqen-2A Discordant SGDP 136,545,769 – 136,714,614 168,845.0 0.02634980 27 103.1254 5,236.3
S_Khomani_San-2B + S_Palestinian-1A Discordant SGDP 136,545,769 – 136,735,800 190,031.0 0.02656575 19 113.4675 3,349.0
S_Khomani_San-2A + S_Hezhen-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Turkish-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Yi-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Mozabite-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Xibo-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Mansi-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Eskimo_Naukan-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Xibo-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Mozabite-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Itelman-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Mansi-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Makrani-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Balochi-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Bulgarian-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Brahui-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Estonian-2A Discordant SGDP 136,545,769 – 136,677,400 131,631.5 0.02548577 18 84.5717 4,256.7
S_Khomani_San-2A + S_Burusho-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_French-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Burusho-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Icelandic-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Punjabi-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Orcadian-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Punjabi-4B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Spanish-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Abkhasian-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + B_Karitiana-3A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Bulgarian-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Pima-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_English-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Eskimo_Sireniki-1B Discordant SGDP 136,545,769 – 136,762,052 216,283.0 0.02778056 27 127.0403 4,250.6
S_Khomani_San-2A + S_English-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Tlingit-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_English-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Naxi-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Estonian-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Uygur-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Estonian-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Kinh-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Finnish-1B Discordant SGDP 136,545,769 – 136,735,800 190,031.0 0.02656575 32 113.4675 5,640.4
S_Khomani_San-2B + S_Chukchi-1B Discordant SGDP 136,545,769 – 136,649,985 104,216.5 0.02152083 18 68.2406 5,275.5
S_Khomani_San-2A + S_Basque-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Somali-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Georgian-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Brahmin-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Greek-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Hazara-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Icelandic-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Punjabi-3B Discordant SGDP 136,545,769 – 136,735,800 190,031.0 0.02656575 22 113.4675 3,877.8
S_Khomani_San-2A + S_Iranian-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Bulgarian-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Sardinian-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_BantuKenya-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Tuscan-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Finnish-3A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Kyrgyz-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Saami-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Norwegian-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_French-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Orcadian-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Hungarian-2A Discordant SGDP 136,545,769 – 136,762,052 216,283.0 0.02778056 30 127.0403 4,722.9
S_Khomani_San-2A + S_Lezgin-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Samaritan-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_North_Ossetian-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Bergamo-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Adygei-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_North_Ossetian-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Spanish-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Spanish-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Turkish-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Tajik-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Yemenite_Jew-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + B_Sardinian-3A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Yemenite_Jew-1B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Saharawi-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + B_Crete-2A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Piapoco-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2A + S_Pima-1A Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Pima-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
S_Khomani_San-2B + S_Mixe-2B Discordant SGDP 136,545,769 – 136,545,787 18.0 0.00000234 4 1.0105 79,167.5
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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