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:
X2131725101
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 10   position  31,725,101  (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 100.0%
0.0%
SAS 100.0%
0.0%
WEA 98.7%
1.3%
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 SGDP178.8 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_Yemenite_Jew-1A + S_Yemenite_Jew-1B Concordant SGDP 30,233,227 – 32,547,632 2,314,405.0 2.87337953 5 1,111.9144 89.9
S_Yemenite_Jew-1B + S_Abkhasian-1A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 8 154.7210 1,034.1
S_Yemenite_Jew-1B + S_Brahui-1A Discordant SGDP 31,548,099 – 32,451,906 903,806.5 0.49759921 48 434.8271 2,207.8
S_Yemenite_Jew-1B + S_Eskimo_Naukan-2B Discordant SGDP 31,687,839 – 31,792,748 104,908.5 0.00292191 5 51.3561 1,947.2
S_Yemenite_Jew-1B + S_Dusun-1B Discordant SGDP 31,687,839 – 31,725,135 37,296.0 0.00078422 3 18.9021 3,174.3
S_Yemenite_Jew-1B + S_Turkish-2B Discordant SGDP 31,412,883 – 31,868,351 455,468.0 0.16508289 14 219.6246 1,274.9
S_Yemenite_Jew-1B + S_Tuscan-2A Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 75 353.1549 4,247.4
S_Yemenite_Jew-1B + S_Iranian-1A Discordant SGDP 31,412,883 – 31,868,351 455,468.0 0.16508289 11 219.6246 1,001.7
S_Yemenite_Jew-1A + S_Han-1A Discordant SGDP 31,697,077 – 31,725,135 28,058.5 0.00033681 3 14.4681 4,147.1
S_Yemenite_Jew-1A + S_Naxi-3A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Yakut-2B Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Even-3B Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Tubalar-2A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 10 154.7210 1,292.6
S_Yemenite_Jew-1A + S_Mongola-1A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 12 154.7210 1,551.2
S_Yemenite_Jew-1A + S_Quechua-1A Discordant SGDP 31,725,090 – 31,792,748 67,658.0 0.00213777 4 33.4758 2,389.8
S_Yemenite_Jew-1B + S_English-2A Discordant SGDP 31,425,216 – 31,868,351 443,135.0 0.15419834 7 213.7048 655.1
S_Yemenite_Jew-1B + S_Basque-1B Discordant SGDP 31,134,695 – 31,795,978 661,282.5 0.24516534 62 318.4156 3,894.3
S_Yemenite_Jew-1A + S_Uygur-1B Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1B + S_Palestinian-3B Discordant SGDP 31,412,883 – 32,451,906 1,039,022.5 0.64286715 67 499.7308 2,681.4
S_Yemenite_Jew-1A + S_Uygur-2B Discordant SGDP 31,134,695 – 32,645,290 1,510,595.0 0.93003548 135 726.0856 3,718.6
S_Yemenite_Jew-1B + S_Lezgin-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 10 154.7210 1,292.6
S_Yemenite_Jew-1A + S_Burmese-2B Discordant SGDP 31,725,090 – 31,744,517 19,427.5 0.00072083 2 10.3252 3,874.0
S_Yemenite_Jew-1B + B_French-3B Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Burmese-1B Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1B + S_Chukchi-1B Discordant SGDP 31,697,077 – 31,791,018 93,941.0 0.00209612 4 46.0917 1,735.7
S_Yemenite_Jew-1A + S_Thai-1B Discordant SGDP 31,548,099 – 31,744,517 196,418.0 0.01229720 7 95.2806 1,469.3
S_Yemenite_Jew-1B + S_Kusunda-1A Discordant SGDP 31,687,839 – 31,792,748 104,908.5 0.00292191 5 51.3561 1,947.2
S_Yemenite_Jew-1A + S_Thai-2A Discordant SGDP 31,092,468 – 31,868,351 775,883.5 0.30627664 71 373.4241 3,802.6
S_Yemenite_Jew-1B + S_Burusho-2A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 7 154.7210 904.9
S_Yemenite_Jew-1A + S_Bougainville-2B Discordant SGDP 31,687,839 – 31,725,135 37,296.0 0.00078422 3 18.9021 3,174.3
S_Yemenite_Jew-1B + S_Bulgarian-1B Discordant SGDP 31,412,883 – 31,868,351 455,468.0 0.16508289 16 219.6246 1,457.0
S_Yemenite_Jew-1A + S_Papuan-8A Discordant SGDP 31,697,077 – 31,725,135 28,058.5 0.00033681 3 14.4681 4,147.1
S_Yemenite_Jew-1B + S_Finnish-1A Discordant SGDP 31,134,695 – 31,725,135 590,440.0 0.24229657 69 284.4112 4,852.1
S_Yemenite_Jew-1A + S_Irula-2A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1B + S_Greek-2B Discordant SGDP 31,725,090 – 31,791,018 65,928.0 0.00175938 3 32.6454 1,837.9
S_Yemenite_Jew-1A + S_Mala-3A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1B + S_Samaritan-1B Discordant SGDP 31,548,099 – 31,795,978 247,878.5 0.01444522 8 119.9817 1,333.5
S_Yemenite_Jew-1A + S_Brahmin-1B Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1B + S_Sardinian-1A Discordant SGDP 31,725,090 – 31,791,018 65,928.0 0.00175938 3 32.6454 1,837.9
S_Yemenite_Jew-1A + S_Madiga-1A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1B + S_Polish-1A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Makrani-1A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1B + S_Tajik-1B Discordant SGDP 31,412,883 – 31,868,351 455,468.0 0.16508289 15 219.6246 1,366.0
S_Yemenite_Jew-1A + S_Kalash-2A Discordant SGDP 31,687,839 – 31,725,135 37,296.0 0.00078422 3 18.9021 3,174.3
S_Yemenite_Jew-1B + S_Yemenite_Jew-2B Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Sindhi-2A Discordant SGDP 31,134,695 – 31,795,978 661,282.5 0.24516534 64 318.4156 4,019.9
S_Yemenite_Jew-1A + S_Zapotec-1B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 10 154.7210 1,292.6
S_Yemenite_Jew-1A + S_Armenian-1A Discordant SGDP 31,412,883 – 31,868,351 455,468.0 0.16508289 14 219.6246 1,274.9
S_Yemenite_Jew-1B + S_Igorot-1A Discordant SGDP 31,548,099 – 33,231,339 1,683,239.5 0.80852987 110 808.9550 2,719.6
S_Yemenite_Jew-1A + S_Bulgarian-1B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 12 154.7210 1,551.2
S_Yemenite_Jew-1B + S_Eskimo_Naukan-1A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Saami-1B Discordant SGDP 31,725,090 – 32,451,906 726,816.0 0.48602283 52 349.8717 2,972.5
S_Yemenite_Jew-1B + S_Khonda_Dora-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 12 146.4030 1,639.3
S_Yemenite_Jew-1A + S_Saami-2B Discordant SGDP 31,725,090 – 31,791,018 65,928.0 0.00175938 3 32.6454 1,837.9
S_Yemenite_Jew-1B + S_Pathan-1A Discordant SGDP 31,725,090 – 31,791,018 65,928.0 0.00175938 3 32.6454 1,837.9
S_Yemenite_Jew-1A + S_Basque-1A Discordant SGDP 31,417,503 – 31,868,351 450,848.5 0.16187775 16 217.4073 1,471.9
S_Yemenite_Jew-1B + S_Makrani-2A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Icelandic-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 8 154.7210 1,034.1
S_Yemenite_Jew-1B + S_Punjabi-1B Discordant SGDP 31,687,839 – 31,725,135 37,296.0 0.00078422 3 18.9021 3,174.3
S_Yemenite_Jew-1A + S_Iranian-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 9 154.7210 1,163.4
S_Yemenite_Jew-1B + S_Armenian-2A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Iraqi_Jew-2A Discordant SGDP 31,725,090 – 31,791,018 65,928.0 0.00175938 3 32.6454 1,837.9
S_Yemenite_Jew-1B + S_Czech-2A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Druze-2B Discordant SGDP 31,548,099 – 32,451,906 903,806.5 0.49759921 55 434.8271 2,529.7
S_Yemenite_Jew-1B + S_Estonian-2B Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_BedouinB-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 7 154.7210 904.9
S_Yemenite_Jew-1B + S_Finnish-1B Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + S_Tuscan-2A Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 75 353.1549 4,247.4
S_Yemenite_Jew-1B + S_Georgian-1A Discordant SGDP 31,092,468 – 31,868,351 775,883.5 0.30627664 69 373.4241 3,695.5
S_Yemenite_Jew-1A + S_Jordanian-2B Discordant SGDP 31,725,090 – 31,744,517 19,427.5 0.00072083 2 10.3252 3,874.0
S_Yemenite_Jew-1B + S_Icelandic-1B Discordant SGDP 31,412,883 – 31,868,351 455,468.0 0.16508289 11 219.6246 1,001.7
S_Yemenite_Jew-1A + S_Orcadian-2A Discordant SGDP 31,725,090 – 31,744,517 19,427.5 0.00072083 2 10.3252 3,874.0
S_Yemenite_Jew-1B + S_Iraqi_Jew-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 13 154.7210 1,680.4
S_Yemenite_Jew-1A + S_Spanish-1B Discordant SGDP 31,412,883 – 31,868,351 455,468.0 0.16508289 14 219.6246 1,274.9
S_Yemenite_Jew-1B + S_Palestinian-2A Discordant SGDP 31,697,077 – 31,744,517 47,440.5 0.00105756 3 23.7714 2,524.0
S_Yemenite_Jew-1A + B_French-3A Discordant SGDP 31,425,216 – 32,451,906 1,026,689.5 0.63198261 27 493.8110 1,093.5
S_Yemenite_Jew-1B + S_Bergamo-2A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1A + B_Sardinian-3B Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1B + S_Sardinian-1B Discordant SGDP 31,134,695 – 31,820,336 685,641.0 0.24612913 18 330.1077 1,090.6
S_Yemenite_Jew-1B + S_Mozabite-1A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1B + S_Jordanian-2A Discordant SGDP 31,697,077 – 31,792,748 95,671.0 0.00247450 4 46.9221 1,705.0
S_Yemenite_Jew-1B + S_Mixe-2B Discordant SGDP 31,412,883 – 31,868,351 455,468.0 0.16508289 6 219.6246 546.4
S_Yemenite_Jew-1B + S_Russian-2A Discordant SGDP 31,725,090 – 31,744,517 19,427.5 0.00072083 2 10.3252 3,874.0
S_Yemenite_Jew-1B + S_Yakut-1B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 9 154.7210 1,163.4
S_Yemenite_Jew-1B + S_North_Ossetian-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 9 185.2250 971.8
S_Yemenite_Jew-1B + S_Ulchi-2A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 11 154.7210 1,421.9
S_Yemenite_Jew-1B + S_Turkish-2A Discordant SGDP 31,421,613 – 31,868,351 446,738.0 0.15917269 12 215.4342 1,114.0
S_Yemenite_Jew-1B + S_Even-2A Discordant SGDP 31,565,428 – 31,725,135 159,707.0 0.00543240 8 77.6594 2,060.3
S_Yemenite_Jew-1B + S_Turkish-1A Discordant SGDP 31,412,883 – 31,868,351 455,468.0 0.16508289 12 219.6246 1,092.8
S_Yemenite_Jew-1B + S_Naxi-2B Discordant SGDP 31,548,099 – 31,744,517 196,418.0 0.01229720 6 95.2806 1,259.4
S_Yemenite_Jew-1B + B_Dai-4A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
S_Yemenite_Jew-1B + S_Tu-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 12 154.7210 1,551.2
S_Yemenite_Jew-1B + S_Pima-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 10 154.7210 1,292.6
S_Yemenite_Jew-1B + S_Korean-2A Discordant SGDP 31,725,090 – 31,725,135 45.5 0.00000008 2 1.0218 39,145.1
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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