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:
X409516062
Alleles:
reference
A
–
alternate
C
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 2   position  109,516,062  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 99.5%
0.5%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 94.0%
6.0%
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 SGDP676.1 generations 95  =  3  +  921.000
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-10B + S_Papuan-7A Concordant SGDP 107,424,094 – 109,583,828 2,159,733.5 1.68964522 18 1,037.6721 346.9
S_Papuan-11A + S_Papuan-7A Concordant SGDP 108,157,125 – 110,259,490 2,102,364.5 1.88140866 22 1,010.1350 435.6
S_Papuan-10B + S_Papuan-11A Concordant SGDP 108,954,234 – 109,583,828 629,593.5 0.30865218 9 303.2049 593.7
S_Papuan-10B + S_Palestinian-3B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Icelandic-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Finnish-3B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-7A + S_Irula-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-7A + S_Lahu-1A Discordant SGDP 109,218,834 – 109,540,064 321,230.0 0.06816910 11 155.1904 1,417.6
S_Papuan-10B + S_Yoruba-1B Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 127 270.6813 9,383.7
S_Papuan-10B + S_Mozabite-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Biaka-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Dai-3A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 24 282.1982 1,700.9
S_Papuan-10B + S_Tlingit-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Tubalar-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Abkhasian-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Adygei-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_She-1B Discordant SGDP 109,448,183 – 109,627,003 178,820.0 0.20960976 8 86.8336 1,842.6
S_Papuan-10B + S_Piapoco-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Burmese-2A Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 111 270.6813 8,201.5
S_Papuan-7A + S_Dusun-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Kinh-2A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 27 282.1982 1,913.5
S_Papuan-7A + B_Yoruba-3A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + B_Australian-3B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 42 323.9289 2,593.2
S_Papuan-10B + S_Estonian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + B_Australian-4B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 40 323.9289 2,469.7
S_Papuan-10B + S_Hungarian-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Bougainville-2A Discordant SGDP 108,013,075 – 109,540,064 1,526,988.5 0.93488279 64 733.9545 1,744.0
S_Papuan-10B + S_Samaritan-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-3B Discordant SGDP 108,013,075 – 109,627,003 1,613,927.5 1.11518217 65 775.6852 1,675.9
S_Papuan-10B + S_Jordanian-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Bougainville-1B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 29 282.1982 2,055.3
S_Papuan-10B + S_Lezgin-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-1B Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 118 270.6813 8,718.7
S_Papuan-10B + B_Crete-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-8B Discordant SGDP 108,954,234 – 110,002,153 1,047,918.5 0.74461388 70 504.0009 2,777.8
S_Papuan-10B + S_Mende-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-10A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 29 323.9289 1,790.5
S_Papuan-7A + S_Cambodian-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-11B Discordant SGDP 108,013,075 – 109,516,070 1,502,995.0 0.92008410 134 722.4376 3,709.7
S_Papuan-7A + S_Japanese-3A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-6B Discordant SGDP 108,954,234 – 110,002,153 1,047,918.5 0.74461388 60 504.0009 2,380.9
S_Papuan-7A + S_Bougainville-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 24 282.1982 1,700.9
S_Papuan-10B + S_Papuan-5B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-7A + S_Iranian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-13B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 27 282.1982 1,913.5
S_Papuan-7A + S_Surui-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-4A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 30 282.1982 2,126.2
S_Papuan-10B + S_Albanian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-4B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 28 282.1982 1,984.4
S_Papuan-10B + S_Finnish-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-14A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 23 282.1982 1,630.1
S_Papuan-10B + S_Greek-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-14B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 18 282.1982 1,275.7
S_Papuan-10B + S_Hungarian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-7B Discordant SGDP 108,954,234 – 109,529,864 575,629.5 0.17566249 13 277.3022 937.6
S_Papuan-10B + S_Iranian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-9A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 27 323.9289 1,667.0
S_Papuan-10B + S_Samaritan-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-9B Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 126 270.6813 9,309.8
S_Papuan-10B + S_Jordanian-3B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-12A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 33 323.9289 2,037.5
S_Papuan-10B + S_Russian-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-12B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 26 282.1982 1,842.7
S_Papuan-10B + S_Saharawi-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Papuan-2B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 29 238.4356 2,432.5
S_Papuan-10B + S_Lezgin-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Gambian-2B Discordant SGDP 109,320,672 – 109,540,064 219,392.0 0.04714178 14 106.3082 2,633.9
S_Papuan-10B + S_Tajik-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Mansi-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + B_Papuan-15A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 33 238.4356 2,768.0
S_Papuan-10B + S_Bengali-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Saharawi-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Bengali-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Surui-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Kapu-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-7A + S_Yakut-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Yadava-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-7A + S_Naxi-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Somali-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-7A + S_Lahu-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Brahmin-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-7A + B_Australian-4A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Madiga-2A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 33 282.1982 2,338.8
S_Papuan-7A + S_Bougainville-2B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 17 282.1982 1,204.8
S_Papuan-10B + S_Luhya-2A Discordant SGDP 109,328,376 – 109,540,064 211,688.0 0.04218591 11 102.6102 2,144.0
S_Papuan-7A + S_Papuan-6A Discordant SGDP 108,954,234 – 109,884,467 930,232.5 0.64442192 23 447.5116 1,027.9
S_Papuan-10B + S_Brahui-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-7A + S_Khonda_Dora-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Balochi-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-7A + S_Bergamo-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Pathan-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-7A + S_Esan-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Punjabi-3B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 33 282.1982 2,338.8
S_Papuan-7A + S_Piapoco-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
S_Papuan-10B + S_Punjabi-4A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 2 1.0151 39,404.2
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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