HumanGenomeDating
Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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1000 Genomes Project
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

Unmatched Variant ID, using internal ID instead:
X436577217
Alleles:
reference
C
–
alternate
G
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 2   position  136,577,217  (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 Joint clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP310.9 generations 95  =  1  +  941.000
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_Papuan-6A + S_Papuan-5A Concordant SGDP 135,343,836 – 138,444,464 3,100,628.0 2.15671756 31 3,214.6755 192.9
S_Papuan-5A + S_Brahmin-2B Discordant SGDP 136,493,766 – 136,785,841 292,075.0 0.04838542 14 179.9043 1,556.4
S_Papuan-5A + S_Eskimo_Naukan-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 48 575.9127 1,666.9
S_Papuan-5A + S_Japanese-1B Discordant SGDP 135,978,431 – 136,785,841 807,409.5 0.08705724 43 458.2023 1,876.9
S_Papuan-6A + S_Mozabite-1A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Turkish-1B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Samaritan-1B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Saami-2A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 16 182.9998 1,748.6
S_Papuan-6A + S_Yi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 37 552.7512 1,338.8
S_Papuan-6A + S_Even-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 39 552.7512 1,411.1
S_Papuan-6A + S_Tlingit-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 15 182.9998 1,639.3
S_Papuan-6A + S_Yakut-2B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-6A + S_Tubalar-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 14 182.9998 1,530.1
S_Papuan-6A + S_Mixtec-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 15 159.8383 1,876.9
S_Papuan-5A + S_English-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-5A + S_Estonian-1B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 14 182.9998 1,530.1
S_Papuan-6A + S_Yi-2B Discordant SGDP 136,489,176 – 136,584,995 95,819.0 0.01495078 6 58.9537 2,035.5
S_Papuan-5A + S_Basque-1B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-6A + S_Tujia-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 46 575.9127 1,597.5
S_Papuan-5A + S_Orcadian-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-6A + S_Mozabite-2A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 18 182.9998 1,967.2
S_Papuan-5A + B_French-3A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 15 182.9998 1,639.3
S_Papuan-6A + S_Uygur-2B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Xibo-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-6A + S_Tu-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 36 575.9127 1,250.2
S_Papuan-5A + S_Papuan-12B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 27 575.9127 937.6
S_Papuan-6A + S_Japanese-3A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 48 575.9127 1,666.9
S_Papuan-5A + S_Mala-2B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-6A + S_Burmese-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 48 575.9127 1,666.9
S_Papuan-5A + S_Atayal-1A Discordant SGDP 135,782,261 – 136,785,841 1,003,579.5 0.09336228 48 557.4080 1,722.3
S_Papuan-6A + S_Ami-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 43 575.9127 1,493.3
S_Papuan-5A + S_English-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-6A + S_Ami-2A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Finnish-3A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-6A + S_Dusun-2A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_French-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-6A + S_Dusun-1B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Icelandic-1B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-6A + S_Papuan-13A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 46 575.9127 1,597.5
S_Papuan-5A + S_Kyrgyz-2B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-6A + S_Papuan-4A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 28 552.7512 1,013.1
S_Papuan-5A + S_Lezgin-2A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 13 182.9998 1,420.8
S_Papuan-6A + S_Itelman-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 40 552.7512 1,447.3
S_Papuan-5A + S_Yemenite_Jew-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-6A + S_Eskimo_Sireniki-2A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Piapoco-1B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-6A + S_Burusho-2B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Tujia-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 56 575.9127 1,944.7
S_Papuan-6A + S_Punjabi-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 15 182.9998 1,639.3
S_Papuan-5A + S_Dai-1A Discordant SGDP 136,556,402 – 136,785,841 229,439.0 0.03828123 8 141.7557 1,128.7
S_Papuan-6A + S_Punjabi-4B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 13 182.9998 1,420.8
S_Papuan-5A + S_Kinh-2B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-6A + S_Bulgarian-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 14 159.8383 1,751.8
S_Papuan-5A + S_Chukchi-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 14 182.9998 1,530.1
S_Papuan-6A + S_BantuKenya-1A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Mansi-2A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 15 182.9998 1,639.3
S_Papuan-6A + S_Estonian-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 13 182.9998 1,420.8
S_Papuan-5A + S_Khonda_Dora-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 60 575.9127 2,083.6
S_Papuan-6A + S_Georgian-2B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Sindhi-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 15 182.9998 1,639.3
S_Papuan-6A + S_Greek-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 11 182.9998 1,202.2
S_Papuan-5A + S_Atayal-1B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 11 182.9998 1,202.2
S_Papuan-6A + S_Kyrgyz-1A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_English-2A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 14 182.9998 1,530.1
S_Papuan-6A + S_Adygei-1B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Estonian-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-6A + S_Adygei-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 16 182.9998 1,748.6
S_Papuan-5A + S_Finnish-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 14 182.9998 1,530.1
S_Papuan-6A + S_Pima-1A Discordant SGDP 136,489,176 – 136,584,995 95,819.0 0.01495078 6 58.9537 2,035.5
S_Papuan-5A + S_Saami-1A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Mongola-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 9 159.8383 1,126.1
S_Papuan-5A + S_French-2A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 13 182.9998 1,420.8
S_Papuan-5A + S_Mongola-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 12 159.8383 1,501.5
S_Papuan-5A + S_Basque-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 182.9998 1,311.5
S_Papuan-5A + S_Altaian-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 46 575.9127 1,597.5
S_Papuan-5A + S_Icelandic-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 13 182.9998 1,420.8
S_Papuan-5A + S_Aleut-2A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Iranian-1A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Cambodian-1B Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Tuscan-2A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Cambodian-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 62 575.9127 2,153.1
S_Papuan-5A + S_Norwegian-1B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 13 182.9998 1,420.8
S_Papuan-5A + S_Naxi-2A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 19 182.9998 2,076.5
S_Papuan-5A + S_Orcadian-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 15 182.9998 1,639.3
S_Papuan-5A + S_Naxi-3B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 61 575.9127 2,118.4
S_Papuan-5A + S_North_Ossetian-1A Discordant SGDP 136,577,201 – 136,577,229 27.5 0.00000096 4 1.0140 78,897.6
S_Papuan-5A + S_Dai-3A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 16 182.9998 1,748.6
S_Papuan-5A + S_Yemenite_Jew-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 14 159.8383 1,751.8
S_Papuan-5A + S_Miao-2A Discordant SGDP 135,978,431 – 136,785,841 807,409.5 0.08705724 40 458.2023 1,746.0
S_Papuan-5A + B_Crete-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 12 159.8383 1,501.5
S_Papuan-5A + S_Oroqen-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 49 575.9127 1,701.6
S_Papuan-5A + S_Saharawi-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 14 182.9998 1,530.1
S_Papuan-5A + S_Uygur-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 14 182.9998 1,530.1
S_Papuan-5A + S_Pima-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 18 159.8383 2,252.3
S_Papuan-5A + S_Xibo-1B Discordant SGDP 135,978,431 – 136,762,052 783,620.5 0.07237876 43 435.0408 1,976.8
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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