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:
X409503686
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 2   position  109,503,686  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 96.0%
4.0%
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 SGDP358.3 generations 94  =  1  +  931.000
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-10A + S_Papuan-14B Concordant SGDP 108,954,234 – 109,583,828 629,593.5 0.30865218 7 550.1266 254.5
S_Papuan-14B + S_Balochi-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Brahmin-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Yadava-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Bengali-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Saharawi-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Russian-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Icelandic-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-10A + S_Papuan-2A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 17 616.1245 551.8
S_Papuan-10A + S_Papuan-12A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 29 616.1245 941.4
S_Papuan-10A + S_Papuan-4A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 30 430.1542 1,394.8
S_Papuan-10A + S_Papuan-1B Discordant SGDP 108,954,234 – 109,503,691 549,457.0 0.16361519 96 395.6315 4,853.0
S_Papuan-10A + S_Papuan-3A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 23 616.1245 746.6
S_Papuan-10A + B_Australian-4A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-10A + S_She-1B Discordant SGDP 109,448,183 – 109,627,003 178,820.0 0.20960976 10 254.5214 785.8
S_Papuan-14B + S_Punjabi-4B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Finnish-3A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-10A + S_Papuan-2B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 28 442.8143 1,264.6
S_Papuan-14B + S_Palestinian-3B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-10A + S_Hungarian-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Adygei-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-10A + B_Papuan-15B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Surui-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-10A + S_Mende-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Irula-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 31 430.1542 1,441.3
S_Papuan-10A + S_Piapoco-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Khonda_Dora-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Mozabite-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Luhya-2A Discordant SGDP 109,328,376 – 109,540,064 211,688.0 0.04218591 11 136.3590 1,613.4
S_Papuan-14B + S_Tubalar-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Punjabi-3A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Yakut-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Estonian-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Lahu-1A Discordant SGDP 109,218,834 – 109,540,064 321,230.0 0.06816910 17 209.7257 1,621.2
S_Papuan-14B + S_Hungarian-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Dai-3A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 25 430.1542 1,162.4
S_Papuan-14B + S_Samaritan-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Biaka-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Jordanian-3B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Lahu-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Saharawi-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Japanese-3A Discordant SGDP 108,954,234 – 109,503,691 549,457.0 0.16361519 135 395.6315 6,824.5
S_Papuan-14B + B_Crete-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Burmese-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Saharawi-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Kinh-2A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 28 430.1542 1,301.9
S_Papuan-10A + S_Tlingit-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + B_Australian-3B Discordant SGDP 107,782,611 – 109,540,064 1,757,452.5 1.22321809 179 1,823.1517 1,963.6
S_Papuan-14B + S_Kapu-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 29 430.1542 1,348.4
S_Papuan-14B + S_Bougainville-2A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 33 430.1542 1,534.3
S_Papuan-14B + S_Yadava-2A Discordant SGDP 108,986,190 – 109,503,691 517,501.5 0.07216023 74 307.1289 4,818.8
S_Papuan-14B + S_Bougainville-2B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 23 430.1542 1,069.4
S_Papuan-14B + S_Mala-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-3B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 24 430.1542 1,115.9
S_Papuan-14B + S_Somali-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Bougainville-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 26 430.1542 1,208.9
S_Papuan-14B + S_Madiga-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Bougainville-1B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 22 430.1542 1,022.9
S_Papuan-14B + S_Brahui-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 31 430.1542 1,441.3
S_Papuan-14B + S_Pathan-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-8A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 25 430.1542 1,162.4
S_Papuan-14B + S_Punjabi-4A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-10B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 20 430.1542 929.9
S_Papuan-14B + S_Albanian-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-11B Discordant SGDP 108,954,234 – 109,503,691 549,457.0 0.16361519 84 395.6315 4,246.4
S_Papuan-14B + S_Finnish-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-6B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 24 430.1542 1,115.9
S_Papuan-14B + S_Greek-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-5B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Hungarian-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-13A Discordant SGDP 108,954,234 – 109,503,691 549,457.0 0.16361519 94 395.6315 4,751.9
S_Papuan-14B + S_Iranian-1B Discordant SGDP 109,336,853 – 109,540,064 203,210.5 0.03795379 9 128.9041 1,396.4
S_Papuan-14B + S_Papuan-13B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 24 430.1542 1,115.9
S_Papuan-14B + S_Samaritan-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-4B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 25 430.1542 1,162.4
S_Papuan-14B + S_Luo-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-14A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 24 430.1542 1,115.9
S_Papuan-14B + S_Jordanian-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-7A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 27 430.1542 1,255.4
S_Papuan-14B + S_Abkhasian-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-7B Discordant SGDP 108,954,234 – 109,529,864 575,629.5 0.17566249 14 417.8322 670.1
S_Papuan-14B + S_Lezgin-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Gambian-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Tajik-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-9A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 24 430.1542 1,115.9
S_Papuan-14B + S_Yoruba-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Papuan-12A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 31 430.1542 1,441.3
S_Papuan-14B + S_Esan-2B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Mozabite-2B Discordant SGDP 109,132,345 – 109,503,691 371,346.0 0.05384405 98 222.3213 8,816.1
S_Papuan-14B + S_Surui-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Mansi-2A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Piapoco-1B Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
S_Papuan-14B + S_Bengali-1A Discordant SGDP 109,503,678 – 109,503,691 13.0 0.00000018 4 1.0064 79,492.8
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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