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:
X2131679949
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 10   position  31,679,949  (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 SGDP86.5 generations 98  =  3  +  951.000
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-5A + S_Papuan-2A Concordant SGDP 31,132,895 – 33,855,187 2,722,292.0 2.01992367 3 1,616.9389 37.1
S_Papuan-3A + S_Papuan-2A Concordant SGDP 31,359,539 – 32,695,551 1,336,011.5 0.93137531 3 746.1002 80.4
S_Papuan-3A + S_Papuan-5A Concordant SGDP 31,359,539 – 32,695,551 1,336,011.5 0.93137531 3 746.1002 80.4
S_Papuan-5A + S_Brahmin-1B Discordant SGDP 31,565,428 – 31,752,325 186,896.5 0.00649238 3 6.1939 9,686.9
S_Papuan-5A + S_Sardinian-1B Discordant SGDP 31,134,695 – 31,697,077 562,381.5 0.24195976 3 194.5678 308.4
S_Papuan-3A + S_Tubalar-1B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-5A + S_Tu-1B Discordant SGDP 31,679,944 – 31,868,351 188,407.0 0.00954113 3 8.6329 6,950.2
S_Papuan-2A + S_Kusunda-1B Discordant SGDP 31,679,944 – 31,868,351 188,407.0 0.00954113 3 8.6329 6,950.2
S_Papuan-2A + S_Kyrgyz-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Uygur-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-2A + S_Kinh-1B Discordant SGDP 31,092,468 – 31,697,077 604,609.0 0.29770134 3 239.1611 250.9
S_Papuan-3A + S_Miao-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_Miao-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_Ulchi-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_Ulchi-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_Ulchi-2A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-5A + S_Spanish-2A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + S_Yi-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-2A + S_Yakut-2B Discordant SGDP 31,679,944 – 31,868,351 188,407.0 0.00954113 3 8.6329 6,950.2
S_Papuan-3A + S_Kinh-2B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-2A + S_Kapu-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Maori-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-2A + S_Czech-2B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + S_Papuan-3B Discordant SGDP 31,134,695 – 31,680,085 545,390.0 0.24099431 3 193.7955 309.6
S_Papuan-2A + B_Sardinian-3A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Papuan-1B Discordant SGDP 31,601,307 – 31,680,085 78,778.5 0.00178886 3 2.4311 24,680.3
S_Papuan-5A + S_Dai-2B Discordant SGDP 31,565,428 – 31,824,938 259,509.5 0.00967891 3 8.7431 6,862.5
S_Papuan-3A + S_Papuan-4A Discordant SGDP 31,073,594 – 31,680,085 606,491.0 0.31831117 3 255.6489 234.7
S_Papuan-5A + S_Thai-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Papuan-14A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-5A + S_Saami-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_Papuan-14B Discordant SGDP 30,953,957 – 31,868,351 914,394.0 0.51304157 3 411.4333 145.8
S_Papuan-5A + S_Chechen-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Papuan-7A Discordant SGDP 31,601,307 – 31,680,085 78,778.5 0.00178886 3 2.4311 24,680.3
S_Papuan-2A + S_Mozabite-1A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + S_Papuan-9A Discordant SGDP 31,079,206 – 31,680,085 600,879.5 0.31209200 3 250.6736 239.4
S_Papuan-2A + S_Tu-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Papuan-9B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-2A + S_Bougainville-2B Discordant SGDP 31,679,944 – 31,752,325 72,380.5 0.00236262 3 2.8901 20,760.6
S_Papuan-3A + S_Papuan-12A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-2A + S_Mala-3B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Chukchi-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-2A + S_Albanian-1A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + S_Mansi-2B Discordant SGDP 31,139,237 – 31,680,085 540,848.5 0.23646187 3 190.1695 315.5
S_Papuan-2A + S_Icelandic-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-5A + S_Even-3A Discordant SGDP 31,134,695 – 31,697,077 562,381.5 0.24195976 3 194.5678 308.4
S_Papuan-2A + S_Polish-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-5A + S_Even-1A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + S_Irula-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Altaian-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-5A + S_Even-2A Discordant SGDP 31,679,944 – 31,868,351 188,407.0 0.00954113 3 8.6329 6,950.2
S_Papuan-3A + S_Brahui-2B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-5A + S_Oroqen-2A Discordant SGDP 31,679,944 – 31,868,351 188,407.0 0.00954113 3 8.6329 6,950.2
S_Papuan-3A + S_Pathan-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-5A + S_Uygur-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Burusho-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-5A + S_Burmese-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_Burusho-2A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-5A + B_Australian-4A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Abkhasian-1B Discordant SGDP 31,565,428 – 31,795,978 230,549.5 0.00830117 3 7.6409 7,852.4
S_Papuan-5A + S_Kalash-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_English-2B Discordant SGDP 31,565,428 – 31,697,077 131,648.5 0.00509559 3 5.0765 11,819.2
S_Papuan-5A + S_Hungarian-2A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + S_Estonian-2A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-5A + S_Orcadian-2A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Estonian-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-5A + S_Lezgin-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Finnish-2B Discordant SGDP 31,134,695 – 31,744,517 609,822.0 0.24301733 3 195.4139 307.0
S_Papuan-5A + B_Dai-4B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_Finnish-1A Discordant SGDP 31,601,307 – 31,680,085 78,778.5 0.00178886 3 2.4311 24,680.3
S_Papuan-2A + S_Mongola-2B Discordant SGDP 31,134,695 – 31,697,077 562,381.5 0.24195976 3 194.5678 308.4
S_Papuan-3A + S_French-1B Discordant SGDP 31,565,428 – 31,697,077 131,648.5 0.00509559 3 5.0765 11,819.2
S_Papuan-2A + S_Naxi-3B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_French-2B Discordant SGDP 31,565,428 – 31,795,978 230,549.5 0.00830117 3 7.6409 7,852.4
S_Papuan-2A + S_Korean-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Georgian-1B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-2A + B_Australian-3B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_Greek-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-2A + S_Bougainville-1B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + S_Druze-1A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-2A + S_Khonda_Dora-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_BedouinB-1A Discordant SGDP 31,601,307 – 31,744,517 143,210.5 0.00381187 3 4.0495 14,816.6
S_Papuan-2A + S_Brahmin-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_Bergamo-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-2A + S_Punjabi-4B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + S_Bergamo-2A Discordant SGDP 31,565,428 – 31,755,646 190,217.5 0.00706091 3 6.6487 9,024.3
S_Papuan-2A + S_Bulgarian-1A Discordant SGDP 31,601,307 – 31,680,085 78,778.5 0.00178886 3 2.4311 24,680.3
S_Papuan-3A + S_Sardinian-2A Discordant SGDP 31,134,695 – 31,680,085 545,390.0 0.24099431 3 193.7955 309.6
S_Papuan-2A + S_Saharawi-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-3A + S_Jordanian-2A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-2A + S_Tuscan-2B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + S_Lezgin-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-2A + S_Kyrgyz-1A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + S_Spanish-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-2A + B_Papuan-15A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-3A + S_Turkish-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 3 1.7727 33,847.4
S_Papuan-2A + S_Pima-2A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 3 1.0003 59,981.8
S_Papuan-3A + B_French-3B Discordant SGDP 31,601,307 – 31,680,085 78,778.5 0.00178886 3 2.4311 24,680.3
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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