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Genealogical Estimation of Variant Age (GEVA)

Inference of the ancestral origin of a genetic variant at a single locus

rs540289005
Alleles:
reference
C
ancestral
alternate
T
derived
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Allele frequency in   SGDP
Sample 98.4%
1.6%
AFR 89.8%
10.2%
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
Age estimation summary Joint clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
 Genomes in SGDP12,011.6 generations 123  =  28  +  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_Ju_hoan_North-2B + S_Khomani_San-2A Concordant SGDP 31,557,66731,824,938 267,270.5 0.01140339 70 138.4125 10,114.7
S_Khomani_San-2A + S_Khomani_San-1B Concordant SGDP 30,998,17731,824,938 826,760.5 0.47080762 52 774.4911 1,342.8
S_Ju_hoan_North-2B + S_Ju_hoan_North-1B Concordant SGDP 31,556,60331,870,414 313,810.5 0.04203703 20 185.2587 2,159.1
S_Ju_hoan_North-1B + S_Ju_hoan_North-3B Concordant SGDP 31,557,66731,951,947 394,280.0 0.25042696 60 390.5960 3,072.2
S_Ju_hoan_North-1B + S_Khomani_San-2A Concordant SGDP 31,557,66731,824,938 267,270.5 0.01140339 56 138.4125 8,091.8
S_Ju_hoan_North-1A + S_Ju_hoan_North-3B Concordant SGDP 31,480,95431,910,782 429,827.5 0.25894213 11 414.4709 530.8
S_Ju_hoan_North-1A + B_Ju_hoan_North-4B Concordant SGDP 31,557,66731,841,841 284,174.0 0.01321669 36 147.9769 4,865.6
S_Ju_hoan_North-2A + S_Ju_hoan_North-1A Concordant SGDP 31,557,66731,906,050 348,382.5 0.13191199 50 273.7532 3,652.9
S_Ju_hoan_North-2A + S_Ju_hoan_North-1B Concordant SGDP 31,068,51533,707,610 2,639,095.5 1.74323778 137 2,662.3561 1,029.2
S_Ju_hoan_North-2A + S_Ju_hoan_North-3A Concordant SGDP 31,557,66731,841,841 284,174.0 0.01321669 33 147.9769 4,460.2
S_Ju_hoan_North-2A + S_Ju_hoan_North-3B Concordant SGDP 31,557,66731,906,050 348,382.5 0.13191199 48 273.7532 3,506.8
S_Ju_hoan_North-3B + S_Khomani_San-1B Concordant SGDP 31,480,95431,910,782 429,827.5 0.25894213 15 414.4709 723.8
S_Ju_hoan_North-3B + S_Khomani_San-2A Concordant SGDP 31,480,95431,824,938 343,983.5 0.04086920 38 198.8074 3,822.8
S_Ju_hoan_North-3B + B_Ju_hoan_North-4B Concordant SGDP 31,557,66731,841,841 284,174.0 0.01321669 33 147.9769 4,460.2
S_Ju_hoan_North-2B + S_Khomani_San-1B Concordant SGDP 31,557,66731,840,315 282,647.5 0.01290321 50 146.9934 6,803.0
S_Ju_hoan_North-2A + B_Ju_hoan_North-4B Concordant SGDP 31,054,92631,870,414 815,488.0 0.38557722 33 700.8960 941.7
S_Ju_hoan_North-1A + S_Ju_hoan_North-3A Concordant SGDP 31,444,03531,870,414 426,379.0 0.16908465 20 340.9296 1,173.3
S_Ju_hoan_North-2A + S_Khomani_San-2A Concordant SGDP 31,557,66731,795,978 238,310.5 0.01002565 43 123.4096 6,968.7
S_Ju_hoan_North-1A + S_Ju_hoan_North-1B Concordant SGDP 31,557,66731,906,050 348,382.5 0.13191199 52 273.7532 3,799.0
S_Ju_hoan_North-2B + S_Ju_hoan_North-3A Concordant SGDP 31,557,66731,840,315 282,647.5 0.01290321 49 146.9934 6,667.0
S_Ju_hoan_North-1A + S_Khomani_San-1B Concordant SGDP 31,107,57532,162,772 1,055,197.0 0.71285433 68 1,077.7780 1,261.9
S_Ju_hoan_North-2B + S_Ju_hoan_North-3B Concordant SGDP 31,557,66731,840,315 282,647.5 0.01290321 45 146.9934 6,122.7
S_Ju_hoan_North-1B + B_Ju_hoan_North-4B Concordant SGDP 31,068,51531,870,414 801,899.0 0.36691039 36 679.4398 1,059.7
S_Ju_hoan_North-2B + S_Ju_hoan_North-1A Concordant SGDP 31,557,66731,840,315 282,647.5 0.01290321 48 146.9934 6,530.9
S_Khomani_San-2A + B_Ju_hoan_North-4B Concordant SGDP 31,557,66731,824,938 267,270.5 0.01140339 59 138.4125 8,525.2
S_Khomani_San-1B + B_Ju_hoan_North-4B Concordant SGDP 31,557,66731,841,841 284,174.0 0.01321669 38 147.9769 5,135.9
S_Ju_hoan_North-3A + S_Ju_hoan_North-3B Concordant SGDP 31,408,34831,870,414 462,066.0 0.19978861 30 382.6226 1,568.1
S_Ju_hoan_North-3A + B_Ju_hoan_North-4B Concordant SGDP 31,557,66731,841,841 284,174.0 0.01321669 37 147.9769 5,000.8
S_Khomani_San-2A + S_Relli-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Yemenite_Jew-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_BedouinB-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Basque-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Bulgarian-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Kalash-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Madiga-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Tu-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Naxi-3B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Aleut-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Even-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Tubalar-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Pima-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Yadava-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Oroqen-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Mala-3A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_She-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Pathan-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Burmese-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Abkhasian-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Thai-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Saami-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Dusun-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Druze-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Chukchi-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Tuscan-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Orcadian-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Turkish-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + B_Australian-4A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + B_French-3A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + S_Papuan-4B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-1B + S_Papuan-5B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + S_Papuan-7A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Tubalar-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + S_Papuan-12A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Even-3B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + S_Brahmin-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Yakut-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + S_Georgian-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Cambodian-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + S_Icelandic-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Han-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + S_Kyrgyz-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Daur-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + S_Russian-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_She-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + S_Spanish-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Korean-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3A + S_Turkish-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Ami-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Mozabite-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + B_Australian-3B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Maori-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Bougainville-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Papuan-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Kapu-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Papuan-7A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Irula-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Mansi-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Mala-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Khonda_Dora-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Brahmin-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Brahui-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Makrani-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Kalash-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Balochi-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Burusho-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Sindhi-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Finnish-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Armenian-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Iranian-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_English-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + S_Chechen-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Saami-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-3B + B_Sardinian-3B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Iranian-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-2A + S_Lezgin-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Druze-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-1A + S_Papuan-4A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Sardinian-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-1A + S_Papuan-9B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Jordanian-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-1A + S_Sardinian-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Tajik-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-1A + S_Polish-1A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Yemenite_Jew-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-1B + S_Papuan-14A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + B_Dai-4B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Ju_hoan_North-1B + S_Papuan-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + B_Papuan-15A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Mixe-2A Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-1B + S_Papuan-3B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Mongola-1B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-1B + S_French-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
S_Khomani_San-2A + S_Mongola-2B Discordant SGDP 31,705,15931,705,229 69.5 0.00000016 4 1.0335 77,407.5
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.