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:
X409503686
Alleles:
reference
A
–
alternate
G
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 2   position  109,503,686  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 96.0%
4.0%
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 G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP501.2 generations 94  =  1  +  931.000
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_Papuan-10A + S_Papuan-14B Concordant SGDP 108,954,234 – 109,583,828 629,593.5 0.30865218 5 303.2049 329.8
S_Papuan-14B + S_Balochi-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Brahmin-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Yadava-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Bengali-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Saharawi-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Russian-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Icelandic-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-10A + S_Papuan-2A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 15 323.9289 926.1
S_Papuan-10A + S_Papuan-12A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 27 323.9289 1,667.0
S_Papuan-10A + S_Papuan-4A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 28 282.1982 1,984.4
S_Papuan-10A + S_Papuan-1B Discordant SGDP 108,954,234 – 109,503,691 549,457.0 0.16361519 94 264.7394 7,101.3
S_Papuan-10A + S_Papuan-3A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 21 323.9289 1,296.6
S_Papuan-10A + B_Australian-4A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-10A + S_She-1B Discordant SGDP 109,448,183 – 109,627,003 178,820.0 0.20960976 8 86.8336 1,842.6
S_Papuan-14B + S_Punjabi-4B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Finnish-3A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-10A + S_Papuan-2B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 26 238.4356 2,180.9
S_Papuan-14B + S_Palestinian-3B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-10A + S_Hungarian-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Adygei-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-10A + B_Papuan-15B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Surui-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-10A + S_Mende-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Irula-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 29 282.1982 2,055.3
S_Papuan-10A + S_Piapoco-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Khonda_Dora-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Mozabite-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Luhya-2A Discordant SGDP 109,328,376 – 109,540,064 211,688.0 0.04218591 9 102.6102 1,754.2
S_Papuan-14B + S_Tubalar-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Punjabi-3A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Yakut-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Estonian-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Lahu-1A Discordant SGDP 109,218,834 – 109,540,064 321,230.0 0.06816910 15 155.1904 1,933.1
S_Papuan-14B + S_Hungarian-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Dai-3A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 23 282.1982 1,630.1
S_Papuan-14B + S_Samaritan-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Biaka-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Jordanian-3B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Lahu-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Saharawi-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Japanese-3A Discordant SGDP 108,954,234 – 109,503,691 549,457.0 0.16361519 133 264.7394 10,047.6
S_Papuan-14B + B_Crete-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Burmese-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Saharawi-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Kinh-2A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 26 282.1982 1,842.7
S_Papuan-10A + S_Tlingit-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + B_Australian-3B Discordant SGDP 107,782,611 – 109,540,064 1,757,452.5 1.22321809 177 844.5772 4,191.4
S_Papuan-14B + S_Kapu-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 27 282.1982 1,913.5
S_Papuan-14B + S_Bougainville-2A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 31 282.1982 2,197.0
S_Papuan-14B + S_Yadava-2A Discordant SGDP 108,986,190 – 109,503,691 517,501.5 0.07216023 72 249.4007 5,773.8
S_Papuan-14B + S_Bougainville-2B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 21 282.1982 1,488.3
S_Papuan-14B + S_Mala-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-3B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 22 282.1982 1,559.2
S_Papuan-14B + S_Somali-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Bougainville-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 24 282.1982 1,700.9
S_Papuan-14B + S_Madiga-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Bougainville-1B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 20 282.1982 1,417.4
S_Papuan-14B + S_Brahui-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 29 282.1982 2,055.3
S_Papuan-14B + S_Pathan-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-8A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 23 282.1982 1,630.1
S_Papuan-14B + S_Punjabi-4A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-10B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 18 282.1982 1,275.7
S_Papuan-14B + S_Albanian-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-11B Discordant SGDP 108,954,234 – 109,503,691 549,457.0 0.16361519 82 264.7394 6,194.8
S_Papuan-14B + S_Finnish-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-6B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 22 282.1982 1,559.2
S_Papuan-14B + S_Greek-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-5B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Hungarian-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-13A Discordant SGDP 108,954,234 – 109,503,691 549,457.0 0.16361519 92 264.7394 6,950.2
S_Papuan-14B + S_Iranian-1B Discordant SGDP 109,336,853 – 109,540,064 203,210.5 0.03795379 7 98.5410 1,420.7
S_Papuan-14B + S_Papuan-13B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 22 282.1982 1,559.2
S_Papuan-14B + S_Samaritan-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-4B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 23 282.1982 1,630.1
S_Papuan-14B + S_Luo-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-14A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 22 282.1982 1,559.2
S_Papuan-14B + S_Jordanian-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-7A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 25 282.1982 1,771.8
S_Papuan-14B + S_Abkhasian-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-7B Discordant SGDP 108,954,234 – 109,529,864 575,629.5 0.17566249 12 277.3022 865.5
S_Papuan-14B + S_Lezgin-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Gambian-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Tajik-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-9A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 22 282.1982 1,559.2
S_Papuan-14B + S_Yoruba-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Papuan-12A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 29 282.1982 2,055.3
S_Papuan-14B + S_Esan-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Mozabite-2B Discordant SGDP 109,132,345 – 109,503,691 371,346.0 0.05384405 96 179.2461 10,711.5
S_Papuan-14B + S_Surui-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Mansi-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Piapoco-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
S_Papuan-14B + S_Bengali-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 2 1.0062 39,751.9
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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