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:
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 Joint clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP439.6 generations 98  =  3  +  951.000
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-5A + S_Papuan-2A Concordant SGDP 31,132,895 – 33,855,187 2,722,292.0 2.01992367 38 2,923.6391 260.0
S_Papuan-3A + S_Papuan-2A Concordant SGDP 31,359,539 – 32,695,551 1,336,011.5 0.93137531 18 1,387.3858 259.5
S_Papuan-3A + S_Papuan-5A Concordant SGDP 31,359,539 – 32,695,551 1,336,011.5 0.93137531 14 1,387.3858 201.8
S_Papuan-5A + S_Brahmin-1B Discordant SGDP 31,565,428 – 31,752,325 186,896.5 0.00649238 14 95.9042 2,919.6
S_Papuan-5A + S_Sardinian-1B Discordant SGDP 31,134,695 – 31,697,077 562,381.5 0.24195976 68 464.5109 2,927.8
S_Papuan-3A + S_Tubalar-1B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-5A + S_Tu-1B Discordant SGDP 31,679,944 – 31,868,351 188,407.0 0.00954113 15 99.0683 3,028.2
S_Papuan-2A + S_Kusunda-1B Discordant SGDP 31,679,944 – 31,868,351 188,407.0 0.00954113 10 99.0683 2,018.8
S_Papuan-2A + S_Kyrgyz-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Uygur-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 19 157.3398 2,415.2
S_Papuan-2A + S_Kinh-1B Discordant SGDP 31,092,468 – 31,697,077 604,609.0 0.29770134 76 529.3734 2,871.3
S_Papuan-3A + S_Miao-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 12 157.3398 1,525.4
S_Papuan-3A + S_Miao-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 11 157.3398 1,398.2
S_Papuan-3A + S_Ulchi-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 15 157.3398 1,906.7
S_Papuan-3A + S_Ulchi-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 12 157.3398 1,525.4
S_Papuan-3A + S_Ulchi-2A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-5A + S_Spanish-2A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + S_Yi-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 15 157.3398 1,906.7
S_Papuan-2A + S_Yakut-2B Discordant SGDP 31,679,944 – 31,868,351 188,407.0 0.00954113 9 99.0683 1,816.9
S_Papuan-3A + S_Kinh-2B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-2A + S_Kapu-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Maori-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-2A + S_Czech-2B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + S_Papuan-3B Discordant SGDP 31,134,695 – 31,680,085 545,390.0 0.24099431 49 455.5827 2,151.1
S_Papuan-2A + B_Sardinian-3A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Papuan-1B Discordant SGDP 31,601,307 – 31,680,085 78,778.5 0.00178886 7 40.2448 3,478.7
S_Papuan-5A + S_Dai-2B Discordant SGDP 31,565,428 – 31,824,938 259,509.5 0.00967891 16 133.3077 2,400.5
S_Papuan-3A + S_Papuan-4A Discordant SGDP 31,073,594 – 31,680,085 606,491.0 0.31831117 69 546.7646 2,523.9
S_Papuan-5A + S_Thai-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Papuan-14A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-5A + S_Saami-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 15 157.3398 1,906.7
S_Papuan-3A + S_Papuan-14B Discordant SGDP 30,953,957 – 31,868,351 914,394.0 0.51304157 91 850.3424 2,140.3
S_Papuan-5A + S_Chechen-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Papuan-7A Discordant SGDP 31,601,307 – 31,680,085 78,778.5 0.00178886 7 40.2448 3,478.7
S_Papuan-2A + S_Mozabite-1A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + S_Papuan-9A Discordant SGDP 31,079,206 – 31,680,085 600,879.5 0.31209200 82 539.0958 3,042.1
S_Papuan-2A + S_Tu-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Papuan-9B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-2A + S_Bougainville-2B Discordant SGDP 31,679,944 – 31,752,325 72,380.5 0.00236262 6 37.6327 3,188.7
S_Papuan-3A + S_Papuan-12A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-2A + S_Mala-3B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Chukchi-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-2A + S_Albanian-1A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + S_Mansi-2B Discordant SGDP 31,139,237 – 31,680,085 540,848.5 0.23646187 83 449.7768 3,690.7
S_Papuan-2A + S_Icelandic-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-5A + S_Even-3A Discordant SGDP 31,134,695 – 31,697,077 562,381.5 0.24195976 65 464.5109 2,798.6
S_Papuan-2A + S_Polish-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-5A + S_Even-1A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + S_Irula-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Altaian-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-5A + S_Even-2A Discordant SGDP 31,679,944 – 31,868,351 188,407.0 0.00954113 16 99.0683 3,230.1
S_Papuan-3A + S_Brahui-2B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-5A + S_Oroqen-2A Discordant SGDP 31,679,944 – 31,868,351 188,407.0 0.00954113 16 99.0683 3,230.1
S_Papuan-3A + S_Pathan-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-5A + S_Uygur-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Burusho-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 13 157.3398 1,652.5
S_Papuan-5A + S_Burmese-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 17 157.3398 2,160.9
S_Papuan-3A + S_Burusho-2A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-5A + B_Australian-4A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Abkhasian-1B Discordant SGDP 31,565,428 – 31,795,978 230,549.5 0.00830117 11 118.3047 1,859.6
S_Papuan-5A + S_Kalash-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 21 157.3398 2,669.4
S_Papuan-3A + S_English-2B Discordant SGDP 31,565,428 – 31,697,077 131,648.5 0.00509559 7 68.2678 2,050.7
S_Papuan-5A + S_Hungarian-2A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + S_Estonian-2A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-5A + S_Orcadian-2A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Estonian-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 14 157.3398 1,779.6
S_Papuan-5A + S_Lezgin-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Finnish-2B Discordant SGDP 31,134,695 – 31,744,517 609,822.0 0.24301733 91 488.1284 3,728.5
S_Papuan-5A + B_Dai-4B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 16 157.3398 2,033.8
S_Papuan-3A + S_Finnish-1A Discordant SGDP 31,601,307 – 31,680,085 78,778.5 0.00178886 6 40.2448 2,981.8
S_Papuan-2A + S_Mongola-2B Discordant SGDP 31,134,695 – 31,697,077 562,381.5 0.24195976 61 464.5109 2,626.4
S_Papuan-3A + S_French-1B Discordant SGDP 31,565,428 – 31,697,077 131,648.5 0.00509559 8 68.2678 2,343.7
S_Papuan-2A + S_Naxi-3B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_French-2B Discordant SGDP 31,565,428 – 31,795,978 230,549.5 0.00830117 10 118.3047 1,690.6
S_Papuan-2A + S_Korean-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Georgian-1B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-2A + B_Australian-3B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 14 157.3398 1,779.6
S_Papuan-3A + S_Greek-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-2A + S_Bougainville-1B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + S_Druze-1A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-2A + S_Khonda_Dora-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 15 157.3398 1,906.7
S_Papuan-3A + S_BedouinB-1A Discordant SGDP 31,601,307 – 31,744,517 143,210.5 0.00381187 6 72.7905 1,648.6
S_Papuan-2A + S_Brahmin-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 23 157.3398 2,923.6
S_Papuan-3A + S_Bergamo-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-2A + S_Punjabi-4B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + S_Bergamo-2A Discordant SGDP 31,565,428 – 31,755,646 190,217.5 0.00706091 10 97.9531 2,041.8
S_Papuan-2A + S_Bulgarian-1A Discordant SGDP 31,601,307 – 31,680,085 78,778.5 0.00178886 6 40.2448 2,981.8
S_Papuan-3A + S_Sardinian-2A Discordant SGDP 31,134,695 – 31,680,085 545,390.0 0.24099431 90 455.5827 3,951.0
S_Papuan-2A + S_Saharawi-1A Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-3A + S_Jordanian-2A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-2A + S_Tuscan-2B Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + S_Lezgin-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-2A + S_Kyrgyz-1A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + S_Spanish-1B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-2A + B_Papuan-15A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 10 157.3398 1,271.1
S_Papuan-3A + S_Turkish-2B Discordant SGDP 31,679,944 – 31,697,077 17,132.5 0.00096583 4 9.9963 8,003.0
S_Papuan-2A + S_Pima-2A Discordant SGDP 31,679,944 – 31,680,085 141.0 0.00000038 4 1.0680 74,907.5
S_Papuan-3A + B_French-3B Discordant SGDP 31,601,307 – 31,680,085 78,778.5 0.00178886 6 40.2448 2,981.8
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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