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:
X436600438
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  136,600,438  (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 Joint clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP2,732.5 generations 95  =  1  +  940.989
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_Dinka-2A + B_Ju_hoan_North-4B Concordant SGDP 136,588,252 – 136,678,814 90,562.0 0.01653930 14 57.7012 4,852.6
B_Ju_hoan_North-4B + S_Iranian-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Georgian-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Saami-2B Discordant SGDP 136,493,766 – 136,600,488 106,722.5 0.01676385 26 65.6379 7,922.3
B_Ju_hoan_North-4B + S_Mozabite-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
S_Dinka-2A + S_Uygur-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Yemenite_Jew-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_North_Ossetian-1A Discordant SGDP 136,493,766 – 136,600,488 106,722.5 0.01676385 29 65.6379 8,836.4
B_Ju_hoan_North-4B + S_Aleut-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Tlingit-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Eskimo_Chaplin-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Mongola-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Mongola-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Mixtec-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Tuscan-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Orcadian-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Cambodian-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Spanish-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Miao-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Saharawi-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Dai-3B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
S_Dinka-2A + S_Mala-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Xibo-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_BantuKenya-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Yi-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_French-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Mozabite-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Icelandic-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Dai-2A Discordant SGDP 136,493,766 – 136,600,488 106,722.5 0.01676385 28 65.6379 8,531.7
B_Ju_hoan_North-4B + S_Bergamo-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Uygur-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Kyrgyz-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Xibo-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Lezgin-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Thai-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Adygei-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Kinh-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Turkish-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Dusun-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + B_French-3B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Papuan-13B Discordant SGDP 136,496,382 – 136,600,488 104,106.0 0.01617428 27 63.9103 8,449.3
B_Ju_hoan_North-4B + S_Piapoco-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Chukchi-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
S_Dinka-2A + S_Gambian-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Mansi-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
S_Dinka-2A + S_Kyrgyz-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Eskimo_Sireniki-2A Discordant SGDP 135,759,069 – 136,600,488 841,419.5 0.07626366 67 465.8923 2,876.2
B_Ju_hoan_North-4B + S_Finnish-3B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Irula-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Saami-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Brahmin-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_French-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Pathan-1B Discordant SGDP 135,768,919 – 136,600,488 831,569.5 0.06456746 62 451.8073 2,744.5
B_Ju_hoan_North-4B + S_Basque-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Balochi-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Greek-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Brahui-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Icelandic-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Makrani-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Druze-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Burusho-1B Discordant SGDP 135,759,069 – 136,600,488 841,419.5 0.07626366 72 465.8923 3,090.8
B_Ju_hoan_North-4B + S_Bergamo-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Hazara-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Jordanian-3B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Sindhi-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Norwegian-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Punjabi-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Orcadian-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Punjabi-3A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Lezgin-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Punjabi-4A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Adygei-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Albanian-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Spanish-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Bulgarian-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Tajik-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Atayal-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Yemenite_Jew-2B Discordant SGDP 136,493,766 – 136,600,488 106,722.5 0.01676385 28 65.6379 8,531.7
B_Ju_hoan_North-4B + S_Czech-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + B_Crete-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_English-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + B_Papuan-15B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_English-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Karitiana-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_English-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
S_Dinka-2A + S_Altaian-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Estonian-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
S_Dinka-2A + S_Japanese-2A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Estonian-1A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
S_Dinka-2A + S_Papuan-9A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Estonian-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
S_Dinka-2A + S_Burusho-2B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Finnish-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
S_Dinka-2A + S_Yemenite_Jew-1B Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
B_Ju_hoan_North-4B + S_Finnish-3A Discordant SGDP 136,600,410 – 136,600,488 78.0 0.00001316 4 1.0480 76,338.2
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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