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:
X436631241
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  136,631,241  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 98.6%
1.4%
AFR 100.0%
0.0%
AMR 88.6%
11.4%
CAS 100.0%
0.0%
EAS 97.9%
2.1%
OCN 100.0%
0.0%
SAS 100.0%
0.0%
WEA 99.3%
0.7%
reference ← allele frequency → alternate
Select clock model
  Mutation clock
  Recombination clock
  Joint clock
Age estimation summary Mutation clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP203.2 generations 114  =  22  +  920.045
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_Zapotec-2B + S_Norwegian-1A Concordant SGDP 135,170,533 – 136,781,557 1,611,024.5 0.67014098 17 774.2918 439.1
S_Cambodian-2A + S_Norwegian-1A Concordant SGDP 136,489,176 – 136,788,485 299,309.0 0.08152040 5 144.6683 691.2
S_Zapotec-2A + S_Norwegian-1A Concordant SGDP 135,727,306 – 136,778,638 1,051,332.0 0.23041732 10 505.6394 395.5
S_Zapotec-2B + S_Cambodian-2A Concordant SGDP 135,755,745 – 136,781,557 1,025,812.0 0.16248506 12 493.3898 486.4
S_Surui-2B + S_Zapotec-2B Concordant SGDP 136,493,766 – 136,781,557 287,791.5 0.04338087 4 139.1399 575.0
S_Surui-2B + S_Norwegian-1A Concordant SGDP 135,542,762 – 136,851,938 1,309,175.5 0.50539489 13 629.4042 413.1
S_Mixe-3B + S_Norwegian-1A Concordant SGDP 135,216,100 – 136,778,638 1,562,537.5 0.59015006 16 751.0180 426.1
S_Surui-2B + S_Mixe-3B Concordant SGDP 135,542,762 – 136,778,638 1,235,875.5 0.33254240 11 594.2202 370.2
S_Mixe-3B + S_Cambodian-2A Concordant SGDP 136,489,176 – 136,778,638 289,461.5 0.04263593 6 139.9415 857.5
S_Mixe-3B + S_Cambodian-2B Concordant SGDP 136,489,176 – 136,778,638 289,461.5 0.04263593 13 139.9415 1,857.9
S_Mixe-3B + S_Zapotec-2B Concordant SGDP 135,216,100 – 136,778,638 1,562,537.5 0.59015006 22 751.0180 585.9
S_Mixe-3B + S_Zapotec-2A Concordant SGDP 135,734,431 – 136,788,083 1,053,652.0 0.25565025 10 506.7530 394.7
S_Mixe-3B + S_Mixe-3A Concordant SGDP 135,727,306 – 136,778,638 1,051,332.0 0.23041732 20 505.6394 791.1
S_Cambodian-2B + S_Norwegian-1A Concordant SGDP 136,489,176 – 136,787,770 298,593.5 0.06994256 12 144.3249 1,662.9
S_Zapotec-2A + S_Zapotec-2B Concordant SGDP 136,493,766 – 136,976,448 482,682.0 0.27212041 5 232.6874 429.8
S_Surui-2B + S_Mixe-3A Concordant SGDP 135,727,306 – 137,123,261 1,395,955.5 0.82218703 21 671.0586 625.9
S_Zapotec-2A + S_Cambodian-2A Concordant SGDP 136,489,176 – 136,778,638 289,461.5 0.04263593 3 139.9415 428.8
S_Surui-2B + S_Zapotec-2A Concordant SGDP 135,734,431 – 136,778,638 1,044,206.5 0.22327073 7 502.2191 278.8
S_Zapotec-2A + S_Cambodian-2B Concordant SGDP 136,489,176 – 136,778,638 289,461.5 0.04263593 8 139.9415 1,143.3
S_Surui-2B + S_Cambodian-2B Concordant SGDP 136,489,176 – 136,787,770 298,593.5 0.06994256 10 144.3249 1,385.8
S_Mixe-3A + S_Norwegian-1A Concordant SGDP 135,727,306 – 136,851,938 1,124,632.0 0.40326981 17 540.8234 628.7
S_Mixe-3A + S_Cambodian-2B Concordant SGDP 136,489,176 – 136,787,770 298,593.5 0.06994256 8 144.3249 1,108.6
S_Surui-2B + S_Punjabi-4B Discordant SGDP 135,597,516 – 137,032,475 1,434,959.0 0.58652654 55 689.7803 1,594.7
S_Norwegian-1A + S_Orcadian-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 14 510.8754 548.1
S_Norwegian-1A + S_Saharawi-2A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Norwegian-1A + S_French-2A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 13 510.4317 509.4
S_Norwegian-1A + S_Iranian-1A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Mixe-3A + S_Tlingit-1A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 41 510.4317 1,606.5
S_Norwegian-1A + S_Finnish-1A Discordant SGDP 135,483,681 – 136,822,338 1,338,657.0 0.42721690 10 643.5554 310.8
S_Cambodian-2A + S_Japanese-1A Discordant SGDP 135,760,398 – 136,785,841 1,025,443.0 0.10255580 11 493.2126 446.1
S_Cambodian-2A + S_Atayal-1B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 4 143.3990 557.9
S_Mixe-3A + S_Balochi-1A Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 46 584.7690 1,573.3
S_Mixe-3A + S_Brahui-1B Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 45 584.7690 1,539.1
S_Mixe-3A + S_Xibo-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 23 493.3566 932.4
S_Mixe-3A + S_Xibo-1A Discordant SGDP 135,344,431 – 136,785,841 1,441,410.0 0.38887572 55 692.8768 1,587.6
S_Mixe-3A + S_Miao-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 32 493.3566 1,297.2
S_Surui-2B + S_Bergamo-2B Discordant SGDP 135,597,516 – 136,976,283 1,378,767.5 0.47786329 33 662.8084 995.8
S_Cambodian-2A + B_Crete-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Surui-2B + B_French-3A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 25 510.4317 979.6
S_Cambodian-2B + S_Miao-2A Discordant SGDP 135,954,725 – 136,785,841 831,115.5 0.08781031 34 399.9354 1,700.3
S_Norwegian-1A + S_Estonian-2A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Cambodian-2B + S_Dusun-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 41 481.9379 1,701.5
S_Norwegian-1A + S_Saami-1A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Cambodian-2B + S_Papuan-5B Discordant SGDP 135,340,792 – 136,646,325 1,305,532.5 0.37249769 50 627.6556 1,593.2
S_Norwegian-1A + S_Basque-1B Discordant SGDP 135,216,236 – 136,821,414 1,605,177.5 0.66362260 13 771.4852 337.0
S_Norwegian-1A + S_Mozabite-1A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Norwegian-1A + S_Norwegian-1B Discordant SGDP 136,023,831 – 136,822,338 798,507.5 0.15669601 23 384.2836 1,197.0
S_Norwegian-1A + S_Dai-3B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Norwegian-1A + S_North_Ossetian-1B Discordant SGDP 135,340,792 – 136,822,338 1,481,546.0 0.46556231 20 712.1421 561.7
S_Norwegian-1A + S_Mozabite-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Surui-2B + S_Maori-1B Discordant SGDP 135,597,516 – 136,976,283 1,378,767.5 0.47786329 40 662.8084 1,207.0
S_Norwegian-1A + S_Sindhi-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 15 510.8754 587.2
S_Surui-2B + S_Finnish-3B Discordant SGDP 135,597,516 – 136,821,414 1,223,898.0 0.32984843 31 588.4710 1,053.6
S_Norwegian-1A + S_Bulgarian-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 39 481.9379 1,618.5
S_Surui-2B + S_Spanish-1B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Norwegian-1A + S_English-2A Discordant SGDP 135,282,993 – 136,822,338 1,539,345.0 0.57421678 21 739.8856 567.7
S_Mixe-3A + S_Makrani-2A Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 45 584.7690 1,539.1
S_Mixe-3A + S_Mongola-2B Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 48 683.2046 1,405.1
S_Cambodian-2A + S_Burmese-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Mixe-3A + S_Czech-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 40 481.9379 1,660.0
S_Cambodian-2A + S_Kyrgyz-1B Discordant SGDP 135,217,238 – 136,785,841 1,568,603.0 0.59179792 51 753.9294 1,352.9
S_Mixe-3A + S_Jordanian-3A Discordant SGDP 135,941,976 – 136,821,414 879,438.0 0.15649117 49 423.1302 2,316.1
S_Cambodian-2B + S_Mixtec-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Mixe-3A + S_Lezgin-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 36 493.3566 1,459.4
S_Cambodian-2B + S_Xibo-1B Discordant SGDP 135,954,725 – 136,762,052 807,326.5 0.07313183 37 388.5167 1,904.7
S_Mixe-3A + S_Lezgin-1B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Cambodian-2B + S_Papuan-6B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Mixe-3A + S_Spanish-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 40 481.9379 1,660.0
S_Cambodian-2B + S_Mala-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Mixe-3A + S_Yemenite_Jew-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Norwegian-1A + S_Aleut-2B Discordant SGDP 135,216,236 – 136,821,414 1,605,177.5 0.66362260 15 771.4852 388.9
S_Mixe-3A + B_Mixe-1A Discordant SGDP 135,171,548 – 136,976,283 1,804,735.0 0.88085387 19 867.2728 438.2
S_Norwegian-1A + S_Chukchi-1A Discordant SGDP 134,729,034 – 136,822,338 2,093,304.0 1.34536020 35 1,005.7859 696.0
S_Mixe-3A + S_Piapoco-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 4 143.3990 557.9
S_Norwegian-1A + S_Brahmin-2B Discordant SGDP 135,778,044 – 136,822,338 1,044,294.5 0.16506012 45 502.2614 1,791.9
S_Mixe-3B + S_Daur-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Norwegian-1A + S_Punjabi-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 17 510.8754 665.5
S_Mixe-3B + S_Yi-2B Discordant SGDP 135,760,098 – 136,631,242 871,144.5 0.07817721 47 419.1494 2,242.6
S_Norwegian-1A + S_English-1B Discordant SGDP 135,216,236 – 136,821,414 1,605,177.5 0.66362260 11 771.4852 285.2
S_Mixe-3B + S_Kinh-2A Discordant SGDP 135,760,098 – 136,761,879 1,001,781.5 0.08799281 33 481.8551 1,369.7
S_Norwegian-1A + S_English-2B Discordant SGDP 135,216,236 – 136,822,338 1,606,102.0 0.66611213 9 771.9290 233.2
S_Mixe-3B + S_Pathan-2A Discordant SGDP 135,760,098 – 136,761,879 1,001,781.5 0.08799281 28 481.8551 1,162.2
S_Norwegian-1A + S_Estonian-1B Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 11 510.4317 431.0
S_Mixe-3B + S_Samaritan-1A Discordant SGDP 135,760,098 – 136,761,879 1,001,781.5 0.08799281 40 481.8551 1,660.3
S_Norwegian-1A + S_Finnish-3B Discordant SGDP 134,765,570 – 136,822,338 2,056,768.5 1.33035284 33 988.2489 667.8
S_Mixe-3B + S_Kyrgyz-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Norwegian-1A + S_Saami-2A Discordant SGDP 135,340,792 – 136,821,414 1,480,621.5 0.46307279 49 711.6983 1,377.0
S_Mixe-3B + S_Piapoco-1A Discordant SGDP 135,760,098 – 136,761,879 1,001,781.5 0.08799281 37 481.8551 1,535.7
S_Norwegian-1A + S_French-2B Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 11 510.4317 431.0
S_Zapotec-2A + S_Yadava-2A Discordant SGDP 136,489,176 – 136,976,283 487,107.0 0.26562788 43 234.8114 3,662.5
S_Norwegian-1A + S_Icelandic-1B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 12 510.8754 469.8
S_Zapotec-2B + S_Zapotec-1A Discordant SGDP 136,493,766 – 137,032,475 538,709.0 0.37317547 34 259.5803 2,619.6
S_Norwegian-1A + S_Tuscan-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 14 510.8754 548.1
S_Zapotec-2B + S_Tubalar-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 28 481.9379 1,162.0
S_Norwegian-1A + S_Orcadian-1B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 17 510.8754 665.5
S_Zapotec-2B + S_Uygur-1A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 9 129.7773 1,387.0
S_Norwegian-1A + S_Polish-1A Discordant SGDP 135,282,993 – 136,822,338 1,539,345.0 0.57421678 15 739.8856 405.5
S_Zapotec-2B + S_Dusun-2A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Norwegian-1A + B_French-3A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 38 510.8754 1,487.6
S_Zapotec-2B + S_Papuan-12B Discordant SGDP 135,636,692 – 136,976,283 1,339,591.0 0.46977193 105 644.0037 3,260.9
S_Surui-2B + S_Mixtec-1A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 14 611.7410 457.7
S_Zapotec-2B + S_Papuan-2A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Surui-2B + S_Hazara-1B Discordant SGDP 135,597,516 – 136,976,283 1,378,767.5 0.47786329 32 662.8084 965.6
S_Zapotec-2B + S_Burusho-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Surui-2B + S_English-1B Discordant SGDP 135,597,516 – 136,822,338 1,224,822.5 0.33233796 29 588.9148 984.9
S_Cambodian-2A + S_Altaian-1A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Surui-2B + S_Greek-2A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Cambodian-2A + S_Miao-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 12 143.3990 1,673.7
S_Surui-2B + S_Orcadian-1B Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 36 584.7690 1,231.3
S_Cambodian-2A + S_Yi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 13 481.9379 539.5
S_Surui-2B + S_Tajik-2B Discordant SGDP 135,597,516 – 136,976,283 1,378,767.5 0.47786329 35 662.8084 1,056.1
S_Cambodian-2A + S_Tujia-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 22 493.3566 891.8
S_Surui-2B + S_Karitiana-1B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 2 1.0017 39,932.9
S_Cambodian-2A + S_Xibo-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 18 481.9379 747.0
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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