HumanGenomeDating
Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
Shared Ancestry Database
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:
X2131722971
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 10   position  31,722,971  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 99.1%
0.9%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 90.0%
10.0%
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 C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP633.1 generations 103  =  7  +  960.714
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_Papuan-7A + B_Papuan-15B Concordant SGDP 31,458,983 – 32,701,643 1,242,659.5 0.86115841 20 597.4766 669.5
S_Papuan-3B + S_Papuan-7A Concordant SGDP 31,444,802 – 32,701,643 1,256,841.0 0.86778012 18 604.2837 595.7
S_Papuan-7B + B_Papuan-15B Concordant SGDP 31,458,983 – 32,701,643 1,242,659.5 0.86115841 22 597.4766 736.4
S_Papuan-1B + B_Papuan-15B Concordant SGDP 31,458,983 – 32,670,507 1,211,524.0 0.83610128 23 582.5315 789.7
S_Papuan-1B + S_Papuan-7B Concordant SGDP 31,095,432 – 33,231,997 2,136,565.0 1.09065267 12 1,026.5512 233.8
S_Papuan-3B + B_Papuan-15B Concordant SGDP 31,496,096 – 33,182,539 1,686,443.0 0.81343221 22 810.4926 542.9
S_Papuan-3B + S_Papuan-1B Concordant SGDP 31,444,802 – 32,671,573 1,226,771.0 0.84317668 20 589.8501 678.1
B_Papuan-15B + S_Mala-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Bougainville-1B Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 9 83.2118 2,163.2
B_Papuan-15B + B_Karitiana-3B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Adygei-1B Discordant SGDP 31,722,925 – 31,841,841 118,916.5 0.00606318 6 58.0799 2,066.1
B_Papuan-15B + S_Iranian-2A Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 2 15.1120 2,646.9
B_Papuan-15B + S_Georgian-1B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
S_Papuan-3B + S_Mozabite-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Punjabi-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_English-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
S_Papuan-3B + S_Tubalar-1A Discordant SGDP 31,041,075 – 31,723,008 681,933.0 0.36393407 77 328.3278 4,690.4
B_Papuan-15B + S_Hungarian-1B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
S_Papuan-3B + B_Australian-4B Discordant SGDP 31,583,614 – 31,744,517 160,903.0 0.00455283 6 78.2334 1,533.9
B_Papuan-15B + S_Russian-1B Discordant SGDP 31,722,925 – 31,744,517 21,592.5 0.00072412 2 11.3644 3,519.8
S_Papuan-3B + S_Papuan-3A Discordant SGDP 31,134,695 – 31,752,325 617,629.5 0.24335655 52 297.4622 3,496.2
B_Papuan-15B + S_Turkish-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
S_Papuan-3B + S_Papuan-5B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Karitiana-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
S_Papuan-3B + S_Papuan-4A Discordant SGDP 31,134,695 – 32,701,105 1,566,410.0 0.97538007 203 752.8768 5,392.6
B_Papuan-15B + S_Kinh-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
S_Papuan-3B + S_Papuan-14B Discordant SGDP 31,134,695 – 31,752,325 617,629.5 0.24335655 68 297.4622 4,572.0
B_Papuan-15B + S_Papuan-5A Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 3 15.1120 3,970.4
S_Papuan-3B + S_Papuan-2B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 11 137.6738 1,598.0
B_Papuan-15B + S_Brahui-2B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 5 137.6738 726.4
S_Papuan-3B + S_Khonda_Dora-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Bulgarian-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
S_Papuan-3B + S_Burusho-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Finnish-3B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 6 137.6738 871.6
S_Papuan-3B + S_Estonian-1B Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 2 15.1120 2,646.9
B_Papuan-15B + S_Hungarian-2A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
S_Papuan-3B + S_French-2A Discordant SGDP 31,106,698 – 31,723,008 616,310.5 0.28806701 77 296.8290 5,188.2
B_Papuan-15B + S_Icelandic-1B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
S_Papuan-3B + S_Bergamo-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Kyrgyz-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
S_Papuan-3B + S_Sardinian-1B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Lezgin-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
S_Papuan-3B + S_Sardinian-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Spanish-2B Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 2 15.1120 2,646.9
S_Papuan-3B + S_Kyrgyz-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + B_Crete-1A Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 5 137.6738 726.4
S_Papuan-3B + S_Chechen-1B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Surui-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
S_Papuan-3B + S_Lezgin-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Piapoco-1B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
S_Papuan-3B + B_Papuan-15A Discordant SGDP 31,134,695 – 31,752,325 617,629.5 0.24335655 59 297.4622 3,966.9
B_Papuan-15B + S_Japanese-1A Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 8 137.6738 1,162.2
S_Papuan-1B + S_Papuan-9A Discordant SGDP 31,583,614 – 31,989,209 405,595.0 0.28178774 16 195.6856 1,635.3
B_Papuan-15B + B_Australian-3B Discordant SGDP 31,722,925 – 31,841,841 118,916.5 0.00606318 4 58.0799 1,377.4
S_Papuan-1B + S_Finnish-1B Discordant SGDP 31,722,925 – 31,868,351 145,426.5 0.00824186 8 70.8047 2,259.7
B_Papuan-15B + S_Papuan-8B Discordant SGDP 31,496,660 – 31,868,351 371,691.0 0.03014480 6 179.4117 668.9
S_Papuan-1B + S_Polish-1A Discordant SGDP 31,722,925 – 31,988,126 265,201.5 0.27147731 18 128.2967 2,806.0
B_Papuan-15B + S_Papuan-2A Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 2 15.1120 2,646.9
S_Papuan-7A + S_Maori-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Brahmin-1B Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 2 15.1120 2,646.9
S_Papuan-7A + S_Papuan-4B Discordant SGDP 31,496,660 – 31,981,099 484,439.0 0.27936222 21 233.5307 1,798.5
B_Papuan-15B + S_Hazara-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
S_Papuan-7A + S_Papuan-12B Discordant SGDP 31,583,614 – 32,420,230 836,616.0 0.47448293 33 402.5757 1,639.4
B_Papuan-15B + S_Abkhasian-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
S_Papuan-7B + S_Mansi-2A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_English-1B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
S_Papuan-7B + S_Kalash-1B Discordant SGDP 31,097,746 – 32,048,924 951,177.5 0.63205012 69 457.5652 3,016.0
B_Papuan-15B + S_Estonian-2B Discordant SGDP 31,722,925 – 31,868,351 145,426.5 0.00824186 7 70.8047 1,977.3
B_Papuan-15B + S_Zapotec-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Saami-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Mixtec-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Greek-1A Discordant SGDP 31,722,925 – 31,868,351 145,426.5 0.00824186 6 70.8047 1,694.8
B_Papuan-15B + S_Mixtec-2A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Hungarian-1A Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 6 129.1814 928.9
B_Papuan-15B + S_Zapotec-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Icelandic-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Quechua-3A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Icelandic-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Quechua-2A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Kyrgyz-2A Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 5 129.1814 774.1
B_Papuan-15B + S_Quechua-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Norwegian-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Tubalar-2A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Russian-2A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Tubalar-1B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 8 137.6738 1,162.2
B_Papuan-15B + S_North_Ossetian-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Yakut-2B Discordant SGDP 31,722,925 – 31,841,841 118,916.5 0.00606318 5 58.0799 1,721.8
B_Papuan-15B + S_Spanish-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Tlingit-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Tajik-1A Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 2 15.1120 2,646.9
B_Papuan-15B + S_Mansi-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Turkish-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Even-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + B_Sardinian-3B Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 3 15.1120 3,970.4
B_Papuan-15B + S_Dai-3B Discordant SGDP 31,379,009 – 31,723,008 343,999.0 0.19085430 21 166.1195 2,528.3
B_Papuan-15B + B_Mixe-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Daur-2A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 2 13.4471 2,974.6
B_Papuan-15B + S_Karitiana-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Tujia-2B Discordant SGDP 31,134,695 – 31,744,517 609,822.0 0.24301733 81 293.7146 5,515.6
B_Papuan-15B + S_Piapoco-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Yi-2B Discordant SGDP 31,722,925 – 31,841,841 118,916.5 0.00606318 5 58.0799 1,721.8
B_Papuan-15B + S_Piapoco-2A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
B_Papuan-15B + S_Tujia-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 2 1.0401 38,458.6
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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