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

Unmatched Variant ID, using internal ID instead:
X409559723
Alleles:
reference
C
–
alternate
T
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 2   position  109,559,723  (GRCh37)
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 Recombination clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP450.0 generations 94  =  1  +  931.000
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_Khomani_San-2A + S_Khomani_San-1A Concordant SGDP 109,471,639 – 109,830,597 358,957.5 0.47106700 3 377.8536 158.8
S_Khomani_San-1A + S_Masai-1A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Hungarian-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_French-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Estonian-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Saharawi-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + B_Sardinian-3A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Tajik-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + S_Lezgin-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + S_Jordanian-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + S_Luo-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + S_Saharawi-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + S_Luhya-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + S_Burmese-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + S_Mbuti-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_BedouinB-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Abkhasian-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + B_Yoruba-3A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + B_Mandenka-3B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + S_Esan-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Mandenka-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + S_Saharawi-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Piapoco-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-2A + S_BantuHerero-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Finnish-3A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Mozabite-1A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Greek-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Tubalar-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Icelandic-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Tubalar-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Masai-1B Discordant SGDP 109,559,712 – 109,568,400 8,688.0 0.00305908 3 3.4473 17,405.1
S_Khomani_San-1A + S_BantuTswana-2B Discordant SGDP 109,559,712 – 109,564,735 5,022.5 0.00256954 3 3.0556 19,635.9
S_Khomani_San-1A + S_Orcadian-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_BantuTswana-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Adygei-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Tlingit-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Ju_hoan_North-1B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Naxi-2A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + B_Mbuti-4B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Biaka-2B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + B_Dinka-3B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Mbuti-3A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Mende-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Mbuti-3B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Surui-1B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Mbuti-2B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-2A + S_Mozabite-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Mbuti-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Finnish-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + B_Australian-4B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_BantuKenya-1B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Mbuti-1B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Georgian-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Gambian-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Masai-2B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Gambian-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Hungarian-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Mansi-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Iranian-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Bengali-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Iranian-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_BantuKenya-2B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Palestinian-3B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Relli-1A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Bergamo-2A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Somali-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Russian-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Yadava-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_North_Ossetian-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Mala-2A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Adygei-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Khonda_Dora-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Ju_hoan_North-1A Discordant SGDP 109,559,712 – 109,564,735 5,022.5 0.00256954 3 3.0556 19,635.9
S_Khomani_San-1A + S_Kusunda-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + B_Crete-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Brahui-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Yoruba-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Pathan-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + B_Ju_hoan_North-4A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Luo-2A Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + B_Yoruba-3A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Sindhi-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Mandenka-1B Discordant SGDP 109,559,712 – 109,568,400 8,688.0 0.00305908 3 3.4473 17,405.1
S_Khomani_San-1A + S_Luo-2B Discordant SGDP 109,559,712 – 109,581,776 22,064.0 0.00919342 3 8.3547 7,181.6
S_Khomani_San-1A + S_Mandenka-2B Discordant SGDP 109,559,712 – 109,564,735 5,022.5 0.00256954 3 3.0556 19,635.9
S_Khomani_San-1A + S_Punjabi-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Mende-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Punjabi-4B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Dinka-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Luhya-1B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Surui-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Saharawi-1A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Piapoco-2B Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
S_Khomani_San-1A + S_Estonian-2A Discordant SGDP 109,559,712 – 109,559,725 12.5 0.00001496 3 1.0120 59,290.4
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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