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:
X436601349
Alleles:
reference
G
–
alternate
A
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 2   position  136,601,349  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 97.7%
2.3%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 100.0%
0.0%
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 Mutation clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP1,538.6 generations 97  =  1  +  960.990
Pairwise results table Mutation clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Dinka-2B + B_Ju_hoan_North-4B Concordant SGDP 136,600,964 – 136,602,042 1,077.5 0.00018191 1 1.5172 13,182.2
S_Dinka-2B + S_Punjabi-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Balochi-1B Discordant SGDP 136,568,364 – 136,649,985 81,621.5 0.01515019 7 40.1783 3,484.5
S_Dinka-2B + S_Mansi-2B Discordant SGDP 136,568,364 – 136,762,052 193,688.0 0.02140992 16 93.9702 3,405.3
S_Dinka-2B + S_Saharawi-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_North_Ossetian-1A Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
S_Dinka-2B + S_Tuscan-2A Discordant SGDP 136,568,364 – 136,762,052 193,688.0 0.02140992 18 93.9702 3,831.0
S_Dinka-2B + S_Saami-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Thai-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Uygur-2B Discordant SGDP 136,473,791 – 136,601,381 127,589.5 0.02046067 27 62.2430 8,675.7
B_Ju_hoan_North-4B + S_Yi-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Xibo-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Tlingit-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Eskimo_Chaplin-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_English-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Estonian-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Kinh-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Icelandic-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Eskimo_Sireniki-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Norwegian-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Irula-1A Discordant SGDP 135,759,069 – 136,601,381 842,312.0 0.07641424 58 405.3098 2,862.0
S_Dinka-2B + S_Turkish-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Pathan-1B Discordant SGDP 135,768,919 – 136,601,381 832,462.0 0.06471804 61 400.5818 3,045.6
S_Dinka-2B + S_Chukchi-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Burusho-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Mala-3B Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
B_Ju_hoan_North-4B + S_Punjabi-3B Discordant SGDP 136,493,766 – 136,601,381 107,615.0 0.01691443 26 52.6552 9,875.6
S_Dinka-2B + S_Hazara-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Albanian-1A Discordant SGDP 135,759,069 – 136,601,381 842,312.0 0.07641424 63 405.3098 3,108.7
S_Dinka-2B + S_Bulgarian-1B Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
B_Ju_hoan_North-4B + S_Atayal-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Estonian-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_BantuKenya-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Finnish-3B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Estonian-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Basque-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Saami-1A Discordant SGDP 135,759,069 – 136,601,381 842,312.0 0.07641424 58 405.3098 2,862.0
S_Dinka-2B + S_Samaritan-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Basque-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Kyrgyz-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Georgian-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Orcadian-2A Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
B_Ju_hoan_North-4B + S_Iranian-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Spanish-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Druze-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Yemenite_Jew-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Orcadian-2A Discordant SGDP 136,489,176 – 136,601,381 112,204.5 0.01803008 27 54.8582 9,843.6
B_Ju_hoan_North-4B + S_Mongola-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Adygei-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Mozabite-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Adygei-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Mala-2B Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
B_Ju_hoan_North-4B + S_Tajik-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Brahmin-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Turkish-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Burusho-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Yemenite_Jew-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Sindhi-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + B_Crete-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Punjabi-4A Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
B_Ju_hoan_North-4B + S_Karitiana-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Czech-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
B_Ju_hoan_North-4B + S_Piapoco-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_English-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Mozabite-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Estonian-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Mixtec-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Finnish-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_BantuHerero-1B Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
S_Dinka-2B + S_Saami-1A Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
S_Dinka-2B + S_Mongola-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_French-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Altaian-1A Discordant SGDP 136,568,364 – 136,762,052 193,688.0 0.02140992 19 93.9702 4,043.8
S_Dinka-2B + S_Greek-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Tubalar-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Icelandic-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Aleut-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Sardinian-1B Discordant SGDP 136,568,364 – 136,762,052 193,688.0 0.02140992 12 93.9702 2,554.0
S_Dinka-2B + S_Cambodian-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Jordanian-3A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Naxi-3A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Kyrgyz-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Miao-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Orcadian-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Oroqen-1B Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
S_Dinka-2B + S_Lezgin-2B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Uygur-1B Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Spanish-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Xibo-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Tajik-2A Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
S_Dinka-2B + S_Dusun-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Yemenite_Jew-2B Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
S_Dinka-2B + S_Dusun-1A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + B_French-3A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Papuan-10A Discordant SGDP 136,568,364 – 136,762,052 193,688.0 0.02140992 15 93.9702 3,192.5
S_Dinka-2B + S_Pima-2A Discordant SGDP 136,601,346 – 136,601,381 34.5 0.00000582 2 1.0166 39,348.4
S_Dinka-2B + S_Papuan-9A Discordant SGDP 136,601,346 – 136,603,542 2,195.5 0.00063857 2 2.0538 19,475.7
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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