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:
X2131629504
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  31,629,504  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 99.5%
0.5%
AFR 97.7%
2.3%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 98.9%
1.1%
OCN 100.0%
0.0%
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 Joint clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP1,304.2 generations 102  =  3  +  990.333
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_Masai-1B + S_Lahu-1A Concordant SGDP 31,601,307 – 31,629,505 28,198.0 0.00082439 4 15.1945 5,265.0
S_Masai-1A + S_Masai-1B Concordant SGDP 31,545,842 – 31,882,796 336,953.5 0.12257388 21 260.7968 1,610.4
S_Masai-1A + S_Lahu-1A Concordant SGDP 31,601,307 – 31,630,246 28,939.5 0.00085186 3 15.5724 3,853.0
S_Lahu-1A + S_Yemenite_Jew-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Piapoco-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1B + S_Kyrgyz-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Hungarian-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1A + S_Spanish-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1B + S_Papuan-5B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Aleut-1B Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 64 430.5324 2,973.1
S_Masai-1A + S_Kalash-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Yakut-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Altaian-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Mongola-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Mongola-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Quechua-3A Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 65 430.5324 3,019.5
S_Masai-1A + S_Even-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Even-3B Discordant SGDP 31,545,842 – 31,900,053 354,210.5 0.12862723 20 273.9228 1,460.3
S_Masai-1A + S_Igorot-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Even-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1A + S_Tuscan-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Tlingit-2B Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 64 430.5324 2,973.1
S_Masai-1B + S_Yakut-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Naxi-3A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1B + S_Estonian-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Tu-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Mixtec-1B Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 82 430.5324 3,809.2
S_Lahu-1A + S_Daur-2B Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 68 430.5324 3,158.9
S_Lahu-1A + S_Iranian-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Oroqen-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + B_Karitiana-3A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Hezhen-1A Discordant SGDP 31,545,842 – 31,868,351 322,509.0 0.02405567 15 175.0489 1,713.8
S_Lahu-1A + S_Pima-1B Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 75 430.5324 3,484.1
S_Lahu-1A + S_Hezhen-2A Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 64 430.5324 2,973.1
S_Masai-1A + S_Papuan-3B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Uygur-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1A + S_Mala-3B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Xibo-1A Discordant SGDP 31,556,184 – 31,841,841 285,657.0 0.01355583 10 148.9600 1,342.6
S_Masai-1A + S_Druze-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Dai-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1A + S_Orcadian-2B Discordant SGDP 31,629,494 – 31,636,829 7,335.0 0.00026541 5 4.7331 21,127.7
S_Lahu-1A + S_Xibo-2A Discordant SGDP 31,134,695 – 31,839,917 705,222.0 0.24796127 75 537.8756 2,788.7
S_Masai-1B + S_Mongola-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Lahu-2B Discordant SGDP 31,081,771 – 31,900,053 818,281.5 0.42222348 80 731.5539 2,187.1
S_Masai-1B + S_Ami-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Naxi-1A Discordant SGDP 31,112,961 – 31,629,505 516,543.5 0.27604933 57 469.7803 2,426.7
S_Masai-1B + S_Papuan-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Abkhasian-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1B + S_French-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Czech-2B Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 70 430.5324 3,251.8
S_Lahu-1A + S_Naxi-1B Discordant SGDP 30,969,229 – 31,900,053 930,823.5 0.60306385 25 930.2464 537.5
S_Lahu-1A + S_Zapotec-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Abkhasian-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_She-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Georgian-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Tu-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Icelandic-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Japanese-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Russian-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Japanese-2A Discordant SGDP 31,134,695 – 31,900,053 765,357.5 0.35510662 83 652.4569 2,544.2
S_Lahu-1A + S_Yemenite_Jew-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Korean-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Karitiana-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Korean-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Pima-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Burmese-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Pima-2A Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 78 430.5324 3,623.4
S_Lahu-1A + S_Ami-2A Discordant SGDP 31,134,695 – 31,841,841 707,146.0 0.24835638 59 539.1152 2,188.8
S_Masai-1A + S_Korean-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Ami-2B Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 86 430.5324 3,995.1
S_Masai-1A + S_Papuan-13A Discordant SGDP 31,556,184 – 31,868,351 312,167.0 0.01573451 26 163.4278 3,181.8
S_Lahu-1A + S_Maori-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1A + S_Eskimo_Sireniki-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Papuan-9A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1A + S_Brahui-2A Discordant SGDP 31,556,184 – 31,868,351 312,167.0 0.01573451 25 163.4278 3,059.5
S_Lahu-1A + S_Igorot-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1A + S_Finnish-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Hawaiian-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1A + S_Sardinian-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Bengali-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1A + S_Jordanian-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Relli-2A Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 74 430.5324 3,437.6
S_Masai-1A + S_Lezgin-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Irula-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1B + S_Mozabite-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Yadava-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1B + S_Tubalar-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Mala-2B Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 60 430.5324 2,787.2
S_Masai-1B + S_Han-1A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Pathan-1B Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 63 430.5324 2,926.6
S_Masai-1B + S_Thai-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Brahui-1B Discordant SGDP 31,134,695 – 31,629,505 494,809.5 0.24002984 82 430.5324 3,809.2
S_Masai-1B + S_Papuan-12B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Hazara-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1B + S_Czech-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Kalash-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1B + S_Saami-1B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Sindhi-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1B + S_Bergamo-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Sindhi-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Masai-1B + S_Yemenite_Jew-2A Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
S_Lahu-1A + S_Punjabi-2B Discordant SGDP 31,629,494 – 31,629,505 10.5 0.00000035 4 1.0053 79,576.7
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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