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 Mutation clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP996.1 generations 95  =  1  +  941.000
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_Papuan-2B + B_Papuan-15A Concordant SGDP 107,325,385 – 109,648,650 2,323,265.5 1.99494542 51 1,116.1674 913.8
B_Papuan-15A + S_BantuTswana-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Surui-1B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Abkhasian-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Tlingit-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
B_Papuan-15A + S_Hungarian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Mala-2B Discordant SGDP 109,591,520 – 109,912,835 321,315.5 0.31463844 54 155.2314 6,957.4
B_Papuan-15A + S_Papuan-5B Discordant SGDP 109,591,520 – 110,096,282 504,762.0 0.49865621 63 243.2858 5,179.1
S_Papuan-2B + S_Lahu-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Dai-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Tujia-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Miao-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Lahu-1A Discordant SGDP 109,218,834 – 109,591,531 372,697.0 0.22437415 21 179.8946 2,334.7
S_Papuan-2B + S_Cambodian-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Miao-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
B_Papuan-15A + S_Lahu-2A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 33 221.4090 2,980.9
S_Papuan-2B + S_She-1B Discordant SGDP 109,448,183 – 109,627,003 178,820.0 0.20960976 8 86.8336 1,842.6
B_Papuan-15A + S_Igorot-2A Discordant SGDP 109,543,810 – 109,912,835 369,025.5 0.38045135 35 178.1322 3,929.7
S_Papuan-2B + S_Burmese-2A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
B_Papuan-15A + S_Finnish-3B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Ami-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Papuan-15A + S_Sardinian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Kinh-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Jordanian-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + B_Australian-3A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Lezgin-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + B_Australian-4A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Piapoco-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Bougainville-2A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 40 221.4090 3,613.2
B_Papuan-15A + S_Lahu-1A Discordant SGDP 109,220,337 – 109,591,531 371,193.5 0.22426093 26 179.1729 2,902.2
S_Papuan-2B + S_Bougainville-2B Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 25 221.4090 2,258.3
B_Papuan-15A + S_Tujia-1A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Papuan-3B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 24 238.4356 2,013.1
B_Papuan-15A + S_Bougainville-1A Discordant SGDP 109,132,345 – 109,884,467 752,121.5 0.53465077 110 362.0183 6,077.0
S_Papuan-2B + S_Bougainville-1A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 37 221.4090 3,342.2
B_Papuan-15A + S_Papuan-2A Discordant SGDP 109,132,345 – 110,096,282 963,936.5 0.73002681 29 463.6895 1,250.8
S_Papuan-2B + S_Papuan-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Papuan-15A + S_Kapu-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Papuan-8A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 23 238.4356 1,929.2
B_Papuan-15A + S_English-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Papuan-8B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 21 238.4356 1,761.5
B_Papuan-15A + S_French-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Papuan-10B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 29 238.4356 2,432.5
B_Papuan-15A + S_Iraqi_Jew-1A Discordant SGDP 109,591,520 – 109,912,835 321,315.5 0.31463844 58 155.2314 7,472.7
S_Papuan-2B + S_Papuan-11A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 30 221.4090 2,709.9
B_Papuan-15A + S_Saharawi-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Papuan-11B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 20.5199 2,924.0
S_Papuan-2B + S_Bergamo-2B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Papuan-6B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 24 238.4356 2,013.1
S_Papuan-2B + S_Russian-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Papuan-5B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Saharawi-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Papuan-13A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 20.5199 2,924.0
S_Papuan-2B + B_Dai-4A Discordant SGDP 109,543,810 – 109,625,961 82,151.5 0.08664363 7 40.4327 3,462.5
S_Papuan-2B + S_Papuan-4A Discordant SGDP 109,132,345 – 110,001,864 869,519.0 0.63236425 51 418.3691 2,438.0
S_Papuan-2B + S_Surui-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Papuan-14A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 45 221.4090 4,064.9
B_Papuan-15A + S_Tubalar-1B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Papuan-14B Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 32 221.4090 2,890.6
B_Papuan-15A + S_Mansi-1A Discordant SGDP 109,591,520 – 109,865,465 273,945.5 0.29862737 60 132.4938 9,057.0
S_Papuan-2B + S_Papuan-7A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 27 221.4090 2,438.9
B_Papuan-15A + S_Dai-3A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 30 221.4090 2,709.9
S_Papuan-2B + S_Papuan-7B Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 66 238.4356 5,536.1
B_Papuan-15A + S_Yi-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
S_Papuan-2B + S_Papuan-9A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 18 238.4356 1,509.8
B_Papuan-15A + S_Uygur-2A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Papuan-12A Discordant SGDP 109,132,345 – 109,627,003 494,657.5 0.25547333 27 238.4356 2,264.8
B_Papuan-15A + S_Kinh-2B Discordant SGDP 109,590,060 – 109,912,835 322,775.0 0.31553087 77 155.9320 9,876.1
S_Papuan-2B + S_Gambian-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Papuan-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
S_Papuan-2B + S_Mozabite-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Papuan-12B Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 47 221.4090 4,245.5
S_Papuan-2B + S_Bengali-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Igorot-1A Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Somali-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Mansi-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Madiga-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Irula-1A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 59 221.4090 5,329.5
S_Papuan-2B + S_Luhya-2A Discordant SGDP 109,328,376 – 109,600,146 271,770.0 0.20237003 23 131.4496 3,499.4
B_Papuan-15A + S_Burusho-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Balochi-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Finnish-2A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Pathan-2A Discordant SGDP 109,132,345 – 109,591,531 459,185.5 0.23137900 69 221.4090 6,232.8
B_Papuan-15A + S_Saami-1B Discordant SGDP 109,590,060 – 109,591,531 1,470.5 0.00090083 2 1.7058 23,448.9
S_Papuan-2B + S_Punjabi-3A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Basque-1A Discordant SGDP 109,591,520 – 109,884,887 293,367.0 0.30437794 62 141.8162 8,743.7
S_Papuan-2B + S_Saharawi-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Icelandic-2B Discordant SGDP 109,591,520 – 109,865,465 273,945.5 0.29862737 68 132.4938 10,264.6
S_Papuan-2B + S_Estonian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Samaritan-1A Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Hungarian-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Adygei-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Hungarian-1B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
B_Papuan-15A + S_Mende-2B Discordant SGDP 109,591,520 – 109,591,531 11.0 0.00000840 2 1.0053 39,789.9
S_Papuan-2B + S_Iranian-1B Discordant SGDP 109,336,853 – 109,591,531 254,677.5 0.19415884 19 123.2452 3,083.3
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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