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 Joint clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP340.8 generations 114  =  22  +  920.409
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_Zapotec-2B + S_Norwegian-1A Concordant SGDP 135,170,533 – 136,781,557 1,611,024.5 0.67014098 19 1,310.4045 290.0
S_Cambodian-2A + S_Norwegian-1A Concordant SGDP 136,489,176 – 136,788,485 299,309.0 0.08152040 7 209.8846 667.0
S_Zapotec-2A + S_Norwegian-1A Concordant SGDP 135,727,306 – 136,778,638 1,051,332.0 0.23041732 12 689.9732 347.8
S_Zapotec-2B + S_Cambodian-2A Concordant SGDP 135,755,745 – 136,781,557 1,025,812.0 0.16248506 14 623.3778 449.2
S_Surui-2B + S_Zapotec-2B Concordant SGDP 136,493,766 – 136,781,557 287,791.5 0.04338087 6 173.8446 690.3
S_Surui-2B + S_Norwegian-1A Concordant SGDP 135,542,762 – 136,851,938 1,309,175.5 0.50539489 15 1,033.7201 290.2
S_Mixe-3B + S_Norwegian-1A Concordant SGDP 135,216,100 – 136,778,638 1,562,537.5 0.59015006 18 1,223.1381 294.3
S_Surui-2B + S_Mixe-3B Concordant SGDP 135,542,762 – 136,778,638 1,235,875.5 0.33254240 13 860.2542 302.2
S_Mixe-3B + S_Cambodian-2A Concordant SGDP 136,489,176 – 136,778,638 289,461.5 0.04263593 8 174.0503 919.3
S_Mixe-3B + S_Cambodian-2B Concordant SGDP 136,489,176 – 136,778,638 289,461.5 0.04263593 15 174.0503 1,723.6
S_Mixe-3B + S_Zapotec-2B Concordant SGDP 135,216,100 – 136,778,638 1,562,537.5 0.59015006 24 1,223.1381 392.4
S_Mixe-3B + S_Zapotec-2A Concordant SGDP 135,734,431 – 136,788,083 1,053,652.0 0.25565025 12 711.2732 337.4
S_Mixe-3B + S_Mixe-3A Concordant SGDP 135,727,306 – 136,778,638 1,051,332.0 0.23041732 22 689.9732 637.7
S_Cambodian-2B + S_Norwegian-1A Concordant SGDP 136,489,176 – 136,787,770 298,593.5 0.06994256 14 200.2789 1,398.1
S_Zapotec-2A + S_Zapotec-2B Concordant SGDP 136,493,766 – 136,976,448 482,682.0 0.27212041 7 450.3837 310.8
S_Surui-2B + S_Mixe-3A Concordant SGDP 135,727,306 – 137,123,261 1,395,955.5 0.82218703 23 1,328.8083 346.2
S_Zapotec-2A + S_Cambodian-2A Concordant SGDP 136,489,176 – 136,778,638 289,461.5 0.04263593 5 174.0503 574.5
S_Surui-2B + S_Zapotec-2A Concordant SGDP 135,734,431 – 136,778,638 1,044,206.5 0.22327073 9 680.8357 264.4
S_Zapotec-2A + S_Cambodian-2B Concordant SGDP 136,489,176 – 136,778,638 289,461.5 0.04263593 10 174.0503 1,149.1
S_Surui-2B + S_Cambodian-2B Concordant SGDP 136,489,176 – 136,787,770 298,593.5 0.06994256 12 200.2789 1,198.3
S_Mixe-3A + S_Norwegian-1A Concordant SGDP 135,727,306 – 136,851,938 1,124,632.0 0.40326981 19 863.4392 440.1
S_Mixe-3A + S_Cambodian-2B Concordant SGDP 136,489,176 – 136,787,770 298,593.5 0.06994256 10 200.2789 998.6
S_Surui-2B + S_Punjabi-4B Discordant SGDP 135,597,516 – 137,032,475 1,434,959.0 0.58652654 57 1,159.0016 983.6
S_Norwegian-1A + S_Orcadian-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 16 649.9127 492.4
S_Norwegian-1A + S_Saharawi-2A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Norwegian-1A + S_French-2A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 15 647.4773 463.3
S_Norwegian-1A + S_Iranian-1A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Mixe-3A + S_Tlingit-1A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 43 647.4773 1,328.2
S_Norwegian-1A + S_Finnish-1A Discordant SGDP 135,483,681 – 136,822,338 1,338,657.0 0.42721690 12 985.3289 243.6
S_Cambodian-2A + S_Japanese-1A Discordant SGDP 135,760,398 – 136,785,841 1,025,443.0 0.10255580 13 575.2573 452.0
S_Cambodian-2A + S_Atayal-1B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 6 182.9998 655.7
S_Mixe-3A + S_Balochi-1A Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 48 840.2265 1,142.5
S_Mixe-3A + S_Brahui-1B Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 47 840.2265 1,118.7
S_Mixe-3A + S_Xibo-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 25 575.9127 868.2
S_Mixe-3A + S_Xibo-1A Discordant SGDP 135,344,431 – 136,785,841 1,441,410.0 0.38887572 57 1,003.9774 1,135.5
S_Mixe-3A + S_Miao-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 34 575.9127 1,180.7
S_Surui-2B + S_Bergamo-2B Discordant SGDP 135,597,516 – 136,976,283 1,378,767.5 0.47786329 35 1,045.0990 669.8
S_Cambodian-2A + B_Crete-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Surui-2B + B_French-3A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 27 647.4773 834.0
S_Cambodian-2B + S_Miao-2A Discordant SGDP 135,954,725 – 136,785,841 831,115.5 0.08781031 36 470.1837 1,531.3
S_Norwegian-1A + S_Estonian-2A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Cambodian-2B + S_Dusun-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 43 552.7512 1,555.9
S_Norwegian-1A + S_Saami-1A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Cambodian-2B + S_Papuan-5B Discordant SGDP 135,340,792 – 136,646,325 1,305,532.5 0.37249769 52 925.6538 1,123.5
S_Norwegian-1A + S_Basque-1B Discordant SGDP 135,216,236 – 136,821,414 1,605,177.5 0.66362260 15 1,302.3833 230.3
S_Norwegian-1A + S_Mozabite-1A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Norwegian-1A + S_Norwegian-1B Discordant SGDP 136,023,831 – 136,822,338 798,507.5 0.15669601 25 509.6404 981.1
S_Norwegian-1A + S_Dai-3B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Norwegian-1A + S_North_Ossetian-1B Discordant SGDP 135,340,792 – 136,822,338 1,481,546.0 0.46556231 22 1,084.5919 405.7
S_Norwegian-1A + S_Mozabite-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Surui-2B + S_Maori-1B Discordant SGDP 135,597,516 – 136,976,283 1,378,767.5 0.47786329 42 1,045.0990 803.8
S_Norwegian-1A + S_Sindhi-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 17 649.9127 523.1
S_Surui-2B + S_Finnish-3B Discordant SGDP 135,597,516 – 136,821,414 1,223,898.0 0.32984843 33 852.3498 774.3
S_Norwegian-1A + S_Bulgarian-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 41 552.7512 1,483.5
S_Surui-2B + S_Spanish-1B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Norwegian-1A + S_English-2A Discordant SGDP 135,282,993 – 136,822,338 1,539,345.0 0.57421678 23 1,199.2590 383.6
S_Mixe-3A + S_Makrani-2A Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 47 840.2265 1,118.7
S_Mixe-3A + S_Mongola-2B Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 50 987.4305 1,012.7
S_Cambodian-2A + S_Burmese-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Mixe-3A + S_Czech-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 42 552.7512 1,519.7
S_Cambodian-2A + S_Kyrgyz-1B Discordant SGDP 135,217,238 – 136,785,841 1,568,603.0 0.59179792 53 1,227.3678 863.6
S_Mixe-3A + S_Jordanian-3A Discordant SGDP 135,941,976 – 136,821,414 879,438.0 0.15649117 51 548.3232 1,860.2
S_Cambodian-2B + S_Mixtec-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Mixe-3A + S_Lezgin-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 38 575.9127 1,319.6
S_Cambodian-2B + S_Xibo-1B Discordant SGDP 135,954,725 – 136,762,052 807,326.5 0.07313183 39 447.0222 1,744.9
S_Mixe-3A + S_Lezgin-1B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Cambodian-2B + S_Papuan-6B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Mixe-3A + S_Spanish-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 42 552.7512 1,519.7
S_Cambodian-2B + S_Mala-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Mixe-3A + S_Yemenite_Jew-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Norwegian-1A + S_Aleut-2B Discordant SGDP 135,216,236 – 136,821,414 1,605,177.5 0.66362260 17 1,302.3833 261.1
S_Mixe-3A + B_Mixe-1A Discordant SGDP 135,171,548 – 136,976,283 1,804,735.0 0.88085387 21 1,571.9559 267.2
S_Norwegian-1A + S_Chukchi-1A Discordant SGDP 134,729,034 – 136,822,338 2,093,304.0 1.34536020 37 2,082.0741 355.4
S_Mixe-3A + S_Piapoco-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 6 182.9998 655.7
S_Norwegian-1A + S_Brahmin-2B Discordant SGDP 135,778,044 – 136,822,338 1,044,294.5 0.16506012 47 634.3095 1,481.9
S_Mixe-3B + S_Daur-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Norwegian-1A + S_Punjabi-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 19 649.9127 584.7
S_Mixe-3B + S_Yi-2B Discordant SGDP 135,760,098 – 136,631,242 871,144.5 0.07817721 49 481.6911 2,034.5
S_Norwegian-1A + S_English-1B Discordant SGDP 135,216,236 – 136,821,414 1,605,177.5 0.66362260 13 1,302.3833 199.6
S_Mixe-3B + S_Kinh-2A Discordant SGDP 135,760,098 – 136,761,879 1,001,781.5 0.08799281 35 552.2494 1,267.5
S_Norwegian-1A + S_English-2B Discordant SGDP 135,216,236 – 136,822,338 1,606,102.0 0.66611213 11 1,304.8187 168.6
S_Mixe-3B + S_Pathan-2A Discordant SGDP 135,760,098 – 136,761,879 1,001,781.5 0.08799281 30 552.2494 1,086.5
S_Norwegian-1A + S_Estonian-1B Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 13 647.4773 401.6
S_Mixe-3B + S_Samaritan-1A Discordant SGDP 135,760,098 – 136,761,879 1,001,781.5 0.08799281 42 552.2494 1,521.1
S_Norwegian-1A + S_Finnish-3B Discordant SGDP 134,765,570 – 136,822,338 2,056,768.5 1.33035284 35 2,052.5311 341.0
S_Mixe-3B + S_Kyrgyz-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Norwegian-1A + S_Saami-2A Discordant SGDP 135,340,792 – 136,821,414 1,480,621.5 0.46307279 51 1,082.1566 942.6
S_Mixe-3B + S_Piapoco-1A Discordant SGDP 135,760,098 – 136,761,879 1,001,781.5 0.08799281 39 552.2494 1,412.4
S_Norwegian-1A + S_French-2B Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 13 647.4773 401.6
S_Zapotec-2A + S_Yadava-2A Discordant SGDP 136,489,176 – 136,976,283 487,107.0 0.26562788 45 447.3137 2,012.0
S_Norwegian-1A + S_Icelandic-1B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 14 649.9127 430.8
S_Zapotec-2B + S_Zapotec-1A Discordant SGDP 136,493,766 – 137,032,475 538,709.0 0.37317547 36 558.1207 1,290.0
S_Norwegian-1A + S_Tuscan-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 16 649.9127 492.4
S_Zapotec-2B + S_Tubalar-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 30 552.7512 1,085.5
S_Norwegian-1A + S_Orcadian-1B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 19 649.9127 584.7
S_Zapotec-2B + S_Uygur-1A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 11 156.7428 1,403.6
S_Norwegian-1A + S_Polish-1A Discordant SGDP 135,282,993 – 136,822,338 1,539,345.0 0.57421678 17 1,199.2590 283.5
S_Zapotec-2B + S_Dusun-2A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Norwegian-1A + B_French-3A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 40 649.9127 1,230.9
S_Zapotec-2B + S_Papuan-12B Discordant SGDP 135,636,692 – 136,976,283 1,339,591.0 0.46977193 107 1,019.8212 2,098.4
S_Surui-2B + S_Mixtec-1A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 16 954.1291 335.4
S_Zapotec-2B + S_Papuan-2A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Surui-2B + S_Hazara-1B Discordant SGDP 135,597,516 – 136,976,283 1,378,767.5 0.47786329 34 1,045.0990 650.7
S_Zapotec-2B + S_Burusho-2B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Surui-2B + S_English-1B Discordant SGDP 135,597,516 – 136,822,338 1,224,822.5 0.33233796 31 854.7852 725.3
S_Cambodian-2A + S_Altaian-1A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Surui-2B + S_Greek-2A Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Cambodian-2A + S_Miao-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 14 182.9998 1,530.1
S_Surui-2B + S_Orcadian-1B Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 38 840.2265 904.5
S_Cambodian-2A + S_Yi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 15 552.7512 542.7
S_Surui-2B + S_Tajik-2B Discordant SGDP 135,597,516 – 136,976,283 1,378,767.5 0.47786329 37 1,045.0990 708.1
S_Cambodian-2A + S_Tujia-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 24 575.9127 833.5
S_Surui-2B + S_Karitiana-1B Discordant SGDP 136,631,239 – 136,631,242 3.5 0.00000115 4 1.0026 79,792.5
S_Cambodian-2A + S_Xibo-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 20 552.7512 723.7
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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