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:
X436603741
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  136,603,741  (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 Mutation clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP1,859.0 generations 93  =  1  +  920.989
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_Ju_hoan_North-2B + S_Ju_hoan_North-3B Concordant SGDP 135,141,319 – 136,603,746 1,462,427.0 0.80653592 52 702.9650 1,479.4
S_Ju_hoan_North-2B + S_BantuKenya-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Estonian-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Czech-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Punjabi-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Ju_hoan_North-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Adygei-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Jordanian-3A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Pathan-1B Discordant SGDP 135,768,919 – 136,762,052 993,133.0 0.08151055 106 477.7038 4,437.9
S_Ju_hoan_North-3B + S_Irula-1B Discordant SGDP 136,559,711 – 136,762,052 202,341.0 0.02182570 26 98.1237 5,299.4
S_Ju_hoan_North-3B + S_Eskimo_Sireniki-2A Discordant SGDP 135,759,069 – 136,762,052 1,002,983.0 0.09320676 114 482.4318 4,726.1
S_Ju_hoan_North-3B + S_Uygur-2B Discordant SGDP 136,473,791 – 136,762,052 288,260.5 0.03725318 32 139.3650 4,592.3
S_Ju_hoan_North-3B + S_Oroqen-2B Discordant SGDP 136,590,087 – 136,750,428 160,340.5 0.01697273 15 77.9634 3,848.0
S_Ju_hoan_North-3B + S_Oroqen-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Basque-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Iranian-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Burusho-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Orcadian-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Punjabi-3B Discordant SGDP 136,493,766 – 136,739,216 245,450.0 0.03252613 26 118.8160 4,376.5
S_Ju_hoan_North-2B + S_Turkish-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Albanian-1A Discordant SGDP 135,759,069 – 136,762,052 1,002,983.0 0.09320676 110 482.4318 4,560.2
S_Ju_hoan_North-2B + S_Karitiana-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Bulgarian-2A Discordant SGDP 136,556,402 – 136,762,052 205,650.0 0.02360275 24 99.7120 4,813.9
S_Ju_hoan_North-2B + S_Bulgarian-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Estonian-2A Discordant SGDP 136,473,791 – 136,677,400 203,609.0 0.03495840 21 98.7323 4,253.9
S_Ju_hoan_North-2B + S_English-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Saami-1A Discordant SGDP 135,759,069 – 136,677,400 918,331.5 0.09091197 96 441.7991 4,345.9
S_Ju_hoan_North-2B + S_Finnish-3A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Hungarian-2B Discordant SGDP 136,555,141 – 136,739,216 184,074.5 0.02483808 21 89.3558 4,700.3
S_Ju_hoan_North-2B + S_French-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Jordanian-3A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Greek-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Orcadian-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 28 131.9802 4,243.1
S_Ju_hoan_North-2B + S_Bergamo-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Ju_hoan_North-2A Discordant SGDP 136,411,978 – 137,134,525 722,547.0 0.65104046 23 347.8226 1,322.5
S_Ju_hoan_North-2B + S_Norwegian-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Spanish-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_North_Ossetian-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Tajik-2A Discordant SGDP 136,494,791 – 136,739,216 244,424.5 0.03228080 28 118.3238 4,732.8
S_Ju_hoan_North-2B + S_Spanish-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + B_Papuan-15B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Yemenite_Jew-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Mozabite-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + B_Ju_hoan_North-4A Discordant SGDP 136,341,972 – 137,040,044 698,072.0 0.42820263 63 336.0746 3,749.2
S_Ju_hoan_North-2B + S_Mixtec-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-3B + S_Eskimo_Chaplin-1A Discordant SGDP 135,759,069 – 136,762,052 1,002,983.0 0.09320676 111 482.4318 4,601.7
S_Ju_hoan_North-2B + S_Mongola-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Punjabi-4A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Tlingit-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Atayal-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Aleut-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_English-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Miao-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Estonian-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Dai-3A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Finnish-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Miao-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Finnish-3B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Uygur-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Saami-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Xibo-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Basque-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Yi-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Georgian-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Dai-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Icelandic-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Xibo-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Druze-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Thai-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Tuscan-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Kinh-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Kyrgyz-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Dusun-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Orcadian-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Chukchi-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Lezgin-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Mozabite-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Adygei-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Mansi-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Spanish-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Brahmin-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Tajik-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Balochi-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Yemenite_Jew-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Brahui-1B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + B_Crete-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Makrani-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + B_French-3B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Burusho-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Saharawi-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Hazara-1A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Piapoco-2A Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
S_Ju_hoan_North-2B + S_Sindhi-2B Discordant SGDP 136,603,726 – 136,603,746 20.5 0.00000016 2 1.0098 39,610.2
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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