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:
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 Joint clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP422.7 generations 95  =  3  +  921.000
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_Papuan-10B + S_Papuan-7A Concordant SGDP 107,424,094 – 109,583,828 2,159,733.5 1.68964522 20 2,389.3883 167.4
S_Papuan-11A + S_Papuan-7A Concordant SGDP 108,157,125 – 110,259,490 2,102,364.5 1.88140866 24 2,515.2619 190.8
S_Papuan-10B + S_Papuan-11A Concordant SGDP 108,954,234 – 109,583,828 629,593.5 0.30865218 11 550.1266 399.9
S_Papuan-10B + S_Palestinian-3B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Icelandic-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Finnish-3B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-7A + S_Irula-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-7A + S_Lahu-1A Discordant SGDP 109,218,834 – 109,540,064 321,230.0 0.06816910 13 209.7257 1,239.7
S_Papuan-10B + S_Yoruba-1B Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 129 406.7984 6,342.2
S_Papuan-10B + S_Mozabite-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Biaka-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Dai-3A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 26 430.1542 1,208.9
S_Papuan-10B + S_Tlingit-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Tubalar-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Abkhasian-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Adygei-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_She-1B Discordant SGDP 109,448,183 – 109,627,003 178,820.0 0.20960976 10 254.5214 785.8
S_Papuan-10B + S_Piapoco-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Burmese-2A Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 113 406.7984 5,555.6
S_Papuan-7A + S_Dusun-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Kinh-2A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 29 430.1542 1,348.4
S_Papuan-7A + B_Yoruba-3A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + B_Australian-3B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 44 616.1245 1,428.3
S_Papuan-10B + S_Estonian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + B_Australian-4B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 42 616.1245 1,363.4
S_Papuan-10B + S_Hungarian-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Bougainville-2A Discordant SGDP 108,013,075 – 109,540,064 1,526,988.5 0.93488279 66 1,481.8607 890.8
S_Papuan-10B + S_Samaritan-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-3B Discordant SGDP 108,013,075 – 109,627,003 1,613,927.5 1.11518217 67 1,667.8309 803.4
S_Papuan-10B + S_Jordanian-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Bougainville-1B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 31 430.1542 1,441.3
S_Papuan-10B + S_Lezgin-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-1B Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 120 406.7984 5,899.7
S_Papuan-10B + B_Crete-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-8B Discordant SGDP 108,954,234 – 110,002,153 1,047,918.5 0.74461388 72 1,099.6920 1,309.5
S_Papuan-10B + S_Mende-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-10A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 31 616.1245 1,006.3
S_Papuan-7A + S_Cambodian-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-11B Discordant SGDP 108,013,075 – 109,516,070 1,502,995.0 0.92008410 136 1,458.5049 1,864.9
S_Papuan-7A + S_Japanese-3A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-6B Discordant SGDP 108,954,234 – 110,002,153 1,047,918.5 0.74461388 62 1,099.6920 1,127.6
S_Papuan-7A + S_Bougainville-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 26 430.1542 1,208.9
S_Papuan-10B + S_Papuan-5B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-7A + S_Iranian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-13B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 29 430.1542 1,348.4
S_Papuan-7A + S_Surui-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-4A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 32 430.1542 1,487.8
S_Papuan-10B + S_Albanian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-4B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 30 430.1542 1,394.8
S_Papuan-10B + S_Finnish-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-14A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 25 430.1542 1,162.4
S_Papuan-10B + S_Greek-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-14B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 20 430.1542 929.9
S_Papuan-10B + S_Hungarian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-7B Discordant SGDP 108,954,234 – 109,529,864 575,629.5 0.17566249 15 417.8322 718.0
S_Papuan-10B + S_Iranian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-9A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 29 616.1245 941.4
S_Papuan-10B + S_Samaritan-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-9B Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 128 406.7984 6,293.0
S_Papuan-10B + S_Jordanian-3B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-12A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 35 616.1245 1,136.1
S_Papuan-10B + S_Russian-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-12B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 28 430.1542 1,301.9
S_Papuan-10B + S_Saharawi-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Papuan-2B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 31 442.8143 1,400.1
S_Papuan-10B + S_Lezgin-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Gambian-2B Discordant SGDP 109,320,672 – 109,540,064 219,392.0 0.04714178 16 144.0216 2,221.9
S_Papuan-10B + S_Tajik-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Mansi-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + B_Papuan-15A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 35 442.8143 1,580.8
S_Papuan-10B + S_Bengali-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Saharawi-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Bengali-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Surui-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Kapu-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-7A + S_Yakut-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Yadava-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-7A + S_Naxi-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Somali-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-7A + S_Lahu-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Brahmin-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-7A + B_Australian-4A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Madiga-2A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 35 430.1542 1,627.3
S_Papuan-7A + S_Bougainville-2B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 19 430.1542 883.4
S_Papuan-10B + S_Luhya-2A Discordant SGDP 109,328,376 – 109,540,064 211,688.0 0.04218591 13 136.3590 1,906.7
S_Papuan-7A + S_Papuan-6A Discordant SGDP 108,954,234 – 109,884,467 930,232.5 0.64442192 25 963.0491 519.2
S_Papuan-10B + S_Brahui-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-7A + S_Khonda_Dora-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Balochi-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-7A + S_Bergamo-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Pathan-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-7A + S_Esan-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Punjabi-3B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 35 430.1542 1,627.3
S_Papuan-7A + S_Piapoco-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
S_Papuan-10B + S_Punjabi-4A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 4 1.0224 78,250.0
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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