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 Recombination clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP113.2 generations 103  =  7  +  960.990
Pairwise results table Recombination 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 3 689.9267 87.0
S_Papuan-3B + S_Papuan-7A Concordant SGDP 31,444,802 – 32,701,643 1,256,841.0 0.86778012 3 695.2241 86.3
S_Papuan-7B + B_Papuan-15B Concordant SGDP 31,458,983 – 32,701,643 1,242,659.5 0.86115841 3 689.9267 87.0
S_Papuan-1B + B_Papuan-15B Concordant SGDP 31,458,983 – 32,670,507 1,211,524.0 0.83610128 3 669.8810 89.6
S_Papuan-1B + S_Papuan-7B Concordant SGDP 31,095,432 – 33,231,997 2,136,565.0 1.09065267 3 873.5221 68.7
S_Papuan-3B + B_Papuan-15B Concordant SGDP 31,496,096 – 33,182,539 1,686,443.0 0.81343221 3 651.7458 92.1
S_Papuan-3B + S_Papuan-1B Concordant SGDP 31,444,802 – 32,671,573 1,226,771.0 0.84317668 3 675.5413 88.8
B_Papuan-15B + S_Mala-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Bougainville-1B Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 3 7.8602 7,633.4
B_Papuan-15B + B_Karitiana-3B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Adygei-1B Discordant SGDP 31,722,925 – 31,841,841 118,916.5 0.00606318 3 5.8505 10,255.5
B_Papuan-15B + S_Iranian-2A Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 3 1.8507 32,420.5
B_Papuan-15B + S_Georgian-1B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
S_Papuan-3B + S_Mozabite-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Punjabi-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_English-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
S_Papuan-3B + S_Tubalar-1A Discordant SGDP 31,041,075 – 31,723,008 681,933.0 0.36393407 3 292.1473 205.4
B_Papuan-15B + S_Hungarian-1B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
S_Papuan-3B + B_Australian-4B Discordant SGDP 31,583,614 – 31,744,517 160,903.0 0.00455283 3 4.6423 12,924.7
B_Papuan-15B + S_Russian-1B Discordant SGDP 31,722,925 – 31,744,517 21,592.5 0.00072412 3 1.5793 37,991.5
S_Papuan-3B + S_Papuan-3A Discordant SGDP 31,134,695 – 31,752,325 617,629.5 0.24335655 3 195.6852 306.6
B_Papuan-15B + S_Turkish-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
S_Papuan-3B + S_Papuan-5B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Karitiana-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
S_Papuan-3B + S_Papuan-4A Discordant SGDP 31,134,695 – 32,701,105 1,566,410.0 0.97538007 3 781.3041 76.8
B_Papuan-15B + S_Kinh-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
S_Papuan-3B + S_Papuan-14B Discordant SGDP 31,134,695 – 31,752,325 617,629.5 0.24335655 3 195.6852 306.6
B_Papuan-15B + S_Papuan-5A Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 3 1.8507 32,420.5
S_Papuan-3B + S_Papuan-2B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
B_Papuan-15B + S_Brahui-2B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
S_Papuan-3B + S_Khonda_Dora-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Bulgarian-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
S_Papuan-3B + S_Burusho-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Finnish-3B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
S_Papuan-3B + S_Estonian-1B Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 3 1.8507 32,420.5
B_Papuan-15B + S_Hungarian-2A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
S_Papuan-3B + S_French-2A Discordant SGDP 31,106,698 – 31,723,008 616,310.5 0.28806701 3 231.4536 259.2
B_Papuan-15B + S_Icelandic-1B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
S_Papuan-3B + S_Bergamo-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Kyrgyz-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
S_Papuan-3B + S_Sardinian-1B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Lezgin-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
S_Papuan-3B + S_Sardinian-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Spanish-2B Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 3 1.8507 32,420.5
S_Papuan-3B + S_Kyrgyz-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + B_Crete-1A Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
S_Papuan-3B + S_Chechen-1B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Surui-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
S_Papuan-3B + S_Lezgin-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Piapoco-1B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
S_Papuan-3B + B_Papuan-15A Discordant SGDP 31,134,695 – 31,752,325 617,629.5 0.24335655 3 195.6852 306.6
B_Papuan-15B + S_Japanese-1A Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
S_Papuan-1B + S_Papuan-9A Discordant SGDP 31,583,614 – 31,989,209 405,595.0 0.28178774 3 226.4302 265.0
B_Papuan-15B + B_Australian-3B Discordant SGDP 31,722,925 – 31,841,841 118,916.5 0.00606318 3 5.8505 10,255.5
S_Papuan-1B + S_Finnish-1B Discordant SGDP 31,722,925 – 31,868,351 145,426.5 0.00824186 3 7.5935 7,901.5
B_Papuan-15B + S_Papuan-8B Discordant SGDP 31,496,660 – 31,868,351 371,691.0 0.03014480 3 25.1158 2,388.9
S_Papuan-1B + S_Polish-1A Discordant SGDP 31,722,925 – 31,988,126 265,201.5 0.27147731 3 218.1818 275.0
B_Papuan-15B + S_Papuan-2A Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 3 1.8507 32,420.5
S_Papuan-7A + S_Maori-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Brahmin-1B Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 3 1.8507 32,420.5
S_Papuan-7A + S_Papuan-4B Discordant SGDP 31,496,660 – 31,981,099 484,439.0 0.27936222 3 224.4898 267.3
B_Papuan-15B + S_Hazara-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
S_Papuan-7A + S_Papuan-12B Discordant SGDP 31,583,614 – 32,420,230 836,616.0 0.47448293 3 380.5863 157.7
B_Papuan-15B + S_Abkhasian-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
S_Papuan-7B + S_Mansi-2A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_English-1B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
S_Papuan-7B + S_Kalash-1B Discordant SGDP 31,097,746 – 32,048,924 951,177.5 0.63205012 3 506.6401 118.4
B_Papuan-15B + S_Estonian-2B Discordant SGDP 31,722,925 – 31,868,351 145,426.5 0.00824186 3 7.5935 7,901.5
B_Papuan-15B + S_Zapotec-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Saami-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Mixtec-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Greek-1A Discordant SGDP 31,722,925 – 31,868,351 145,426.5 0.00824186 3 7.5935 7,901.5
B_Papuan-15B + S_Mixtec-2A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Hungarian-1A Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 3 10.0637 5,962.0
B_Papuan-15B + S_Zapotec-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Icelandic-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Quechua-3A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Icelandic-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Quechua-2A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Kyrgyz-2A Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 3 10.0637 5,962.0
B_Papuan-15B + S_Quechua-2B Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Norwegian-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Tubalar-2A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Russian-2A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Tubalar-1B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
B_Papuan-15B + S_North_Ossetian-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Yakut-2B Discordant SGDP 31,722,925 – 31,841,841 118,916.5 0.00606318 3 5.8505 10,255.5
B_Papuan-15B + S_Spanish-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Tlingit-2B Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Tajik-1A Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 3 1.8507 32,420.5
B_Papuan-15B + S_Mansi-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Turkish-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Even-1A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + B_Sardinian-3B Discordant SGDP 31,722,925 – 31,752,325 29,400.0 0.00106335 3 1.8507 32,420.5
B_Papuan-15B + S_Dai-3B Discordant SGDP 31,379,009 – 31,723,008 343,999.0 0.19085430 3 153.6834 390.4
B_Papuan-15B + B_Mixe-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Daur-2A Discordant SGDP 31,697,077 – 31,723,008 25,931.5 0.00033352 3 1.2668 47,362.8
B_Papuan-15B + S_Karitiana-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Tujia-2B Discordant SGDP 31,134,695 – 31,744,517 609,822.0 0.24301733 3 195.4139 307.0
B_Papuan-15B + S_Piapoco-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Yi-2B Discordant SGDP 31,722,925 – 31,841,841 118,916.5 0.00606318 3 5.8505 10,255.5
B_Papuan-15B + S_Piapoco-2A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
B_Papuan-15B + S_Tujia-1A Discordant SGDP 31,722,925 – 31,723,008 83.5 0.00000008 3 1.0001 59,996.2
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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