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:
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 Recombination clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP36.3 generations 95  =  1  +  941.000
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-2B + B_Papuan-15A Concordant SGDP 107,325,385 – 109,648,650 2,323,265.5 1.99494542 3 1,596.9563 37.6
B_Papuan-15A + S_BantuTswana-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Surui-1B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Abkhasian-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Tlingit-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
B_Papuan-15A + S_Hungarian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Mala-2B Discordant SGDP 109,591,520 – 109,912,835 321,315.5 0.31463844 3 252.7108 237.4
B_Papuan-15A + S_Papuan-5B Discordant SGDP 109,591,520 – 110,096,282 504,762.0 0.49865621 3 399.9250 150.0
S_Papuan-2B + S_Lahu-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Dai-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Tujia-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Miao-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Lahu-1A Discordant SGDP 109,218,834 – 109,591,531 372,697.0 0.22437415 3 180.4993 332.4
S_Papuan-2B + S_Cambodian-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Miao-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
B_Papuan-15A + S_Lahu-2A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
S_Papuan-2B + S_She-1B Discordant SGDP 109,448,183 – 109,627,003 178,820.0 0.20960976 3 168.6878 355.7
B_Papuan-15A + S_Igorot-2A Discordant SGDP 109,543,810 – 109,912,835 369,025.5 0.38045135 3 305.3611 196.5
S_Papuan-2B + S_Burmese-2A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
B_Papuan-15A + S_Finnish-3B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Ami-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Papuan-15A + S_Sardinian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Kinh-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Jordanian-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + B_Australian-3A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Lezgin-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + B_Australian-4A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Piapoco-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Bougainville-2A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
B_Papuan-15A + S_Lahu-1A Discordant SGDP 109,220,337 – 109,591,531 371,193.5 0.22426093 3 180.4087 332.6
S_Papuan-2B + S_Bougainville-2B Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
B_Papuan-15A + S_Tujia-1A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Papuan-3B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 3 205.3787 292.1
B_Papuan-15A + S_Bougainville-1A Discordant SGDP 109,132,345 – 109,884,467 752,121.5 0.53465077 3 428.7206 140.0
S_Papuan-2B + S_Bougainville-1A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
B_Papuan-15A + S_Papuan-2A Discordant SGDP 109,132,345 – 110,096,282 963,936.5 0.73002681 3 585.0214 102.6
S_Papuan-2B + S_Papuan-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Papuan-15A + S_Kapu-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Papuan-8A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 3 205.3787 292.1
B_Papuan-15A + S_English-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Papuan-8B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 3 205.3787 292.1
B_Papuan-15A + S_French-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Papuan-10B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 3 205.3787 292.1
B_Papuan-15A + S_Iraqi_Jew-1A Discordant SGDP 109,591,520 – 109,912,835 321,315.5 0.31463844 3 252.7108 237.4
S_Papuan-2B + S_Papuan-11A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
B_Papuan-15A + S_Saharawi-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Papuan-11B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-2B + S_Bergamo-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Papuan-6B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 3 205.3787 292.1
S_Papuan-2B + S_Russian-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Papuan-5B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Saharawi-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Papuan-13A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-2B + B_Dai-4A Discordant SGDP 109,543,810 – 109,625,961 82,151.5 0.08664363 3 70.3149 853.3
S_Papuan-2B + S_Papuan-4A Discordant SGDP 109,132,345 – 110,001,864 869,519.0 0.63236425 3 506.8914 118.4
S_Papuan-2B + S_Surui-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Papuan-14A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
B_Papuan-15A + S_Tubalar-1B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Papuan-14B Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
B_Papuan-15A + S_Mansi-1A Discordant SGDP 109,591,520 – 109,865,465 273,945.5 0.29862737 3 239.9019 250.1
S_Papuan-2B + S_Papuan-7A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
B_Papuan-15A + S_Dai-3A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
S_Papuan-2B + S_Papuan-7B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 3 205.3787 292.1
B_Papuan-15A + S_Yi-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-2B + S_Papuan-9A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 3 205.3787 292.1
B_Papuan-15A + S_Uygur-2A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Papuan-12A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 3 205.3787 292.1
B_Papuan-15A + S_Kinh-2B Discordant SGDP 109,590,060 – 109,912,835 322,775.0 0.31553087 3 253.4247 236.8
S_Papuan-2B + S_Gambian-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Papuan-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-2B + S_Mozabite-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Papuan-12B Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
S_Papuan-2B + S_Bengali-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Igorot-1A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Somali-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Mansi-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Madiga-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Irula-1A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
S_Papuan-2B + S_Luhya-2A Discordant SGDP 109,328,376 – 109,600,146 271,770.0 0.20237003 3 162.8960 368.3
B_Papuan-15A + S_Burusho-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Balochi-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Finnish-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Pathan-2A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 3 186.1032 322.4
B_Papuan-15A + S_Saami-1B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 3 1.7207 34,870.3
S_Papuan-2B + S_Punjabi-3A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Basque-1A Discordant SGDP 109,591,520 – 109,884,887 293,367.0 0.30437794 3 244.5024 245.4
S_Papuan-2B + S_Saharawi-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Icelandic-2B Discordant SGDP 109,591,520 – 109,865,465 273,945.5 0.29862737 3 239.9019 250.1
S_Papuan-2B + S_Estonian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Samaritan-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Hungarian-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Adygei-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Hungarian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
B_Papuan-15A + S_Mende-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 3 1.0067 59,599.5
S_Papuan-2B + S_Iranian-1B Discordant SGDP 109,336,853 – 109,591,531 254,677.5 0.19415884 3 156.3271 383.8
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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