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 Recombination clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP37.9 generations 95  =  3  +  920.667
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-10B + S_Papuan-7A Concordant SGDP 107,424,094 – 109,583,828 2,159,733.5 1.68964522 3 1,352.7162 44.4
S_Papuan-11A + S_Papuan-7A Concordant SGDP 108,157,125 – 110,259,490 2,102,364.5 1.88140866 3 1,506.1269 39.8
S_Papuan-10B + S_Papuan-11A Concordant SGDP 108,954,234 – 109,583,828 629,593.5 0.30865218 3 247.9217 242.0
S_Papuan-10B + S_Palestinian-3B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Icelandic-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Finnish-3B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-7A + S_Irula-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-7A + S_Lahu-1A Discordant SGDP 109,218,834 – 109,540,064 321,230.0 0.06816910 3 55.5353 1,080.4
S_Papuan-10B + S_Yoruba-1B Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 3 137.1171 437.6
S_Papuan-10B + S_Mozabite-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Biaka-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Dai-3A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-10B + S_Tlingit-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Tubalar-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Abkhasian-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Adygei-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_She-1B Discordant SGDP 109,448,183 – 109,627,003 178,820.0 0.20960976 3 168.6878 355.7
S_Papuan-10B + S_Piapoco-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Burmese-2A Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 3 137.1171 437.6
S_Papuan-7A + S_Dusun-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Kinh-2A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-7A + B_Yoruba-3A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + B_Australian-3B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 3 293.1956 204.6
S_Papuan-10B + S_Estonian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + B_Australian-4B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 3 293.1956 204.6
S_Papuan-10B + S_Hungarian-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Bougainville-2A Discordant SGDP 108,013,075 – 109,540,064 1,526,988.5 0.93488279 3 748.9062 80.1
S_Papuan-10B + S_Samaritan-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-3B Discordant SGDP 108,013,075 – 109,627,003 1,613,927.5 1.11518217 3 893.1457 67.2
S_Papuan-10B + S_Jordanian-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Bougainville-1B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-10B + S_Lezgin-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-1B Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 3 137.1171 437.6
S_Papuan-10B + B_Crete-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-8B Discordant SGDP 108,954,234 – 110,002,153 1,047,918.5 0.74461388 3 596.6911 100.6
S_Papuan-10B + S_Mende-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-10A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 3 293.1956 204.6
S_Papuan-7A + S_Cambodian-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-11B Discordant SGDP 108,013,075 – 109,516,070 1,502,995.0 0.92008410 3 737.0673 81.4
S_Papuan-7A + S_Japanese-3A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-6B Discordant SGDP 108,954,234 – 110,002,153 1,047,918.5 0.74461388 3 596.6911 100.6
S_Papuan-7A + S_Bougainville-1A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-10B + S_Papuan-5B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-7A + S_Iranian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-13B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-7A + S_Surui-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-4A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-10B + S_Albanian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-4B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-10B + S_Finnish-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-14A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-10B + S_Greek-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-14B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-10B + S_Hungarian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-7B Discordant SGDP 108,954,234 – 109,529,864 575,629.5 0.17566249 3 141.5300 423.9
S_Papuan-10B + S_Iranian-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-9A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 3 293.1956 204.6
S_Papuan-10B + S_Samaritan-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-9B Discordant SGDP 108,954,234 – 109,516,070 561,836.0 0.17014640 3 137.1171 437.6
S_Papuan-10B + S_Jordanian-3B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-12A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 3 293.1956 204.6
S_Papuan-10B + S_Russian-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-12B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-10B + S_Saharawi-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Papuan-2B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 3 205.3787 292.1
S_Papuan-10B + S_Lezgin-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Gambian-2B Discordant SGDP 109,320,672 – 109,540,064 219,392.0 0.04714178 3 38.7134 1,549.9
S_Papuan-10B + S_Tajik-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Mansi-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + B_Papuan-15A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 3 205.3787 292.1
S_Papuan-10B + S_Bengali-1A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Saharawi-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Bengali-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Surui-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Kapu-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-7A + S_Yakut-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Yadava-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-7A + S_Naxi-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Somali-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-7A + S_Lahu-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Brahmin-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-7A + B_Australian-4A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Madiga-2A Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-7A + S_Bougainville-2B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-10B + S_Luhya-2A Discordant SGDP 109,328,376 – 109,540,064 211,688.0 0.04218591 3 34.7487 1,726.7
S_Papuan-7A + S_Papuan-6A Discordant SGDP 108,954,234 – 109,884,467 930,232.5 0.64442192 3 516.5375 116.2
S_Papuan-10B + S_Brahui-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-7A + S_Khonda_Dora-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Balochi-1B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-7A + S_Bergamo-2A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Pathan-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-7A + S_Esan-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Punjabi-3B Discordant SGDP 108,954,234 – 109,540,064 585,829.5 0.18494510 3 148.9561 402.8
S_Papuan-7A + S_Piapoco-2B Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
S_Papuan-10B + S_Punjabi-4A Discordant SGDP 109,516,039 – 109,516,070 31.5 0.00000906 3 1.0072 59,568.5
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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