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:
X409591530
Alleles:
reference
C
–
alternate
A
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 2   position  109,591,530  (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 A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP459.8 generations 95  =  1  +  941.000
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-2B + B_Papuan-15A Concordant SGDP 107,325,385 – 109,648,650 2,323,265.5 1.99494542 53 2,712.1238 390.8
B_Papuan-15A + S_BantuTswana-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Surui-1B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Abkhasian-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Tlingit-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
B_Papuan-15A + S_Hungarian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Mala-2B Discordant SGDP 109,591,520 – 109,912,835 321,315.5 0.31463844 56 406.9422 2,752.2
B_Papuan-15A + S_Papuan-5B Discordant SGDP 109,591,520 – 110,096,282 504,762.0 0.49865621 65 642.2107 2,024.3
S_Papuan-2B + S_Lahu-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Dai-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Tujia-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Miao-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Lahu-1A Discordant SGDP 109,218,834 – 109,591,531 372,697.0 0.22437415 23 359.3939 1,279.9
S_Papuan-2B + S_Cambodian-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Miao-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
B_Papuan-15A + S_Lahu-2A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 35 406.5122 1,722.0
S_Papuan-2B + S_She-1B Discordant SGDP 109,448,183 – 109,627,003 178,820.0 0.20960976 10 254.5214 785.8
B_Papuan-15A + S_Igorot-2A Discordant SGDP 109,543,810 – 109,912,835 369,025.5 0.38045135 37 482.4933 1,533.7
S_Papuan-2B + S_Burmese-2A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
B_Papuan-15A + S_Finnish-3B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Ami-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Papuan-15A + S_Sardinian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Kinh-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Jordanian-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + B_Australian-3A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Lezgin-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + B_Australian-4A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Piapoco-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Bougainville-2A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 42 406.5122 2,066.4
B_Papuan-15A + S_Lahu-1A Discordant SGDP 109,220,337 – 109,591,531 371,193.5 0.22426093 28 358.5816 1,561.7
S_Papuan-2B + S_Bougainville-2B Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 27 406.5122 1,328.4
B_Papuan-15A + S_Tujia-1A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Papuan-3B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 26 442.8143 1,174.3
B_Papuan-15A + S_Bougainville-1A Discordant SGDP 109,132,345 – 109,884,467 752,121.5 0.53465077 112 789.7389 2,836.4
S_Papuan-2B + S_Bougainville-1A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 39 406.5122 1,918.8
B_Papuan-15A + S_Papuan-2A Discordant SGDP 109,132,345 – 110,096,282 963,936.5 0.73002681 31 1,047.7110 591.8
S_Papuan-2B + S_Papuan-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Papuan-15A + S_Kapu-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Papuan-8A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 25 442.8143 1,129.1
B_Papuan-15A + S_English-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Papuan-8B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 23 442.8143 1,038.8
B_Papuan-15A + S_French-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Papuan-10B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 31 442.8143 1,400.1
B_Papuan-15A + S_Iraqi_Jew-1A Discordant SGDP 109,591,520 – 109,912,835 321,315.5 0.31463844 60 406.9422 2,948.8
S_Papuan-2B + S_Papuan-11A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 32 406.5122 1,574.4
B_Papuan-15A + S_Saharawi-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Papuan-11B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 5 42.9729 2,327.0
S_Papuan-2B + S_Bergamo-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Papuan-6B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 26 442.8143 1,174.3
S_Papuan-2B + S_Russian-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Papuan-5B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Saharawi-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Papuan-13A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 5 42.9729 2,327.0
S_Papuan-2B + B_Dai-4A Discordant SGDP 109,543,810 – 109,625,961 82,151.5 0.08664363 9 109.7476 1,640.1
S_Papuan-2B + S_Papuan-4A Discordant SGDP 109,132,345 – 110,001,864 869,519.0 0.63236425 53 924.2605 1,146.9
S_Papuan-2B + S_Surui-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Papuan-14A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 47 406.5122 2,312.4
B_Papuan-15A + S_Tubalar-1B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Papuan-14B Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 34 406.5122 1,672.8
B_Papuan-15A + S_Mansi-1A Discordant SGDP 109,591,520 – 109,865,465 273,945.5 0.29862737 62 371.3957 3,338.8
S_Papuan-2B + S_Papuan-7A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 29 406.5122 1,426.8
B_Papuan-15A + S_Dai-3A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 32 406.5122 1,574.4
S_Papuan-2B + S_Papuan-7B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 68 442.8143 3,071.3
B_Papuan-15A + S_Yi-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
S_Papuan-2B + S_Papuan-9A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 20 442.8143 903.3
B_Papuan-15A + S_Uygur-2A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Papuan-12A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 29 442.8143 1,309.8
B_Papuan-15A + S_Kinh-2B Discordant SGDP 109,590,060 – 109,912,835 322,775.0 0.31553087 79 408.3567 3,869.2
S_Papuan-2B + S_Gambian-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Papuan-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
S_Papuan-2B + S_Mozabite-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Papuan-12B Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 49 406.5122 2,410.8
S_Papuan-2B + S_Bengali-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Igorot-1A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Somali-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Mansi-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Madiga-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Irula-1A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 61 406.5122 3,001.1
S_Papuan-2B + S_Luhya-2A Discordant SGDP 109,328,376 – 109,600,146 271,770.0 0.20237003 25 293.3456 1,704.5
B_Papuan-15A + S_Burusho-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Balochi-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Finnish-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Pathan-2A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 71 406.5122 3,493.1
B_Papuan-15A + S_Saami-1B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 4 2.4265 32,969.3
S_Papuan-2B + S_Punjabi-3A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Basque-1A Discordant SGDP 109,591,520 – 109,884,887 293,367.0 0.30437794 64 385.3185 3,321.9
S_Papuan-2B + S_Saharawi-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Icelandic-2B Discordant SGDP 109,591,520 – 109,865,465 273,945.5 0.29862737 70 371.3957 3,769.6
S_Papuan-2B + S_Estonian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Samaritan-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Hungarian-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Adygei-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Hungarian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
B_Papuan-15A + S_Mende-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 4 1.0120 79,051.4
S_Papuan-2B + S_Iranian-1B Discordant SGDP 109,336,853 – 109,591,531 254,677.5 0.19415884 21 278.5723 1,507.7
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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