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:
X2131805167
Alleles:
reference
C
–
alternate
T
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 10   position  31,805,167  (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 T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP367.7 generations 97  =  1  +  961.000
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-14B + B_Papuan-15A Concordant SGDP 31,073,224 – 32,677,369 1,604,145.0 1.03566464 13 770.9896 337.2
S_Papuan-14B + S_Albanian-1A Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
S_Papuan-14B + S_Punjabi-4A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 13 146.4030 1,775.9
S_Papuan-14B + S_Pathan-1B Discordant SGDP 31,565,428 – 31,805,190 239,762.0 0.00890710 10 116.0858 1,722.9
B_Papuan-15A + S_Sardinian-1A Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Piapoco-2A Discordant SGDP 31,795,978 – 31,820,336 24,358.5 0.00096379 2 12.6921 3,151.6
S_Papuan-14B + S_Jordanian-1B Discordant SGDP 31,792,748 – 31,820,336 27,588.5 0.00169487 2 14.2425 2,808.5
S_Papuan-14B + S_Iraqi_Jew-2A Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Even-3A Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Ulchi-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 11 185.2250 1,187.7
S_Papuan-14B + S_Ulchi-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 11 146.4030 1,502.7
S_Papuan-14B + S_Altaian-1B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 13 185.2250 1,403.7
S_Papuan-14B + S_Tubalar-2B Discordant SGDP 31,792,748 – 31,824,938 32,190.0 0.00210881 2 16.4512 2,431.4
S_Papuan-14B + S_Quechua-1B Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
S_Papuan-14B + S_English-2A Discordant SGDP 31,795,978 – 31,820,336 24,358.5 0.00096379 2 12.6921 3,151.6
S_Papuan-14B + S_Saami-1B Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 52 353.1549 2,944.9
S_Papuan-14B + S_Yakut-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 15 146.4030 2,049.1
S_Papuan-14B + S_Palestinian-1A Discordant SGDP 31,805,070 – 31,805,190 120.0 0.00000026 2 1.0576 37,821.5
S_Papuan-14B + S_Cambodian-2A Discordant SGDP 31,134,695 – 31,805,190 670,495.0 0.24577127 50 322.8376 3,097.5
S_Papuan-14B + B_Dai-4B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 11 146.4030 1,502.7
S_Papuan-14B + S_Naxi-3A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 11 185.2250 1,187.7
B_Papuan-15A + S_Papuan-4A Discordant SGDP 31,073,594 – 31,805,190 731,596.0 0.32308813 53 352.1661 3,009.9
S_Papuan-14B + S_Han-2A Discordant SGDP 31,792,748 – 31,805,190 12,442.5 0.00133701 2 6.9724 5,736.9
S_Papuan-14B + S_Kusunda-1B Discordant SGDP 31,687,839 – 31,824,938 137,098.5 0.00503072 5 66.8073 1,496.8
S_Papuan-14B + S_Miao-1B Discordant SGDP 31,565,543 – 31,868,351 302,808.0 0.01341798 16 146.3478 2,186.6
S_Papuan-14B + S_Kalash-2A Discordant SGDP 31,805,070 – 31,820,336 15,266.0 0.00035812 2 8.3277 4,803.3
S_Papuan-14B + S_Dai-3B Discordant SGDP 31,484,549 – 31,824,938 340,388.5 0.02840148 13 164.3865 1,581.6
S_Papuan-14B + S_Luhya-1A Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Han-1B Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Atayal-1B Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
S_Papuan-14B + S_Tu-2A Discordant SGDP 31,805,070 – 31,805,190 120.0 0.00000026 2 1.0576 37,821.5
S_Papuan-14B + S_Finnish-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 12 146.4030 1,639.3
S_Papuan-14B + S_Uygur-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 18 185.2250 1,943.6
S_Papuan-14B + S_Basque-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 13 146.4030 1,775.9
S_Papuan-14B + S_Yi-1B Discordant SGDP 31,792,748 – 31,805,190 12,442.5 0.00133701 2 6.9724 5,736.9
S_Papuan-14B + S_Iraqi_Jew-1B Discordant SGDP 31,792,748 – 31,805,190 12,442.5 0.00133701 2 6.9724 5,736.9
S_Papuan-14B + S_Yi-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 13 146.4030 1,775.9
S_Papuan-14B + S_Bergamo-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 11 146.4030 1,502.7
S_Papuan-14B + S_Dai-2A Discordant SGDP 31,484,549 – 31,824,938 340,388.5 0.02840148 11 164.3865 1,338.3
S_Papuan-14B + S_North_Ossetian-1A Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Dai-2B Discordant SGDP 31,565,428 – 31,824,938 259,509.5 0.00967891 10 125.5646 1,592.8
S_Papuan-14B + S_Chane-1A Discordant SGDP 31,795,978 – 31,820,336 24,358.5 0.00096379 2 12.6921 3,151.6
S_Papuan-14B + S_Uygur-2B Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
B_Papuan-15A + S_Tubalar-1A Discordant SGDP 31,139,237 – 31,805,190 665,953.5 0.24123883 60 320.6577 3,742.3
S_Papuan-14B + S_She-2B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 10 185.2250 1,079.8
B_Papuan-15A + S_Papuan-9A Discordant SGDP 31,079,206 – 31,805,190 725,984.5 0.31686896 55 349.4726 3,147.6
S_Papuan-14B + S_Korean-2A Discordant SGDP 31,565,428 – 32,448,679 883,250.5 0.48747853 63 424.9602 2,965.0
S_Papuan-14B + S_Quechua-1A Discordant SGDP 31,795,978 – 31,820,336 24,358.5 0.00096379 2 12.6921 3,151.6
S_Papuan-14B + S_Korean-2B Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Kusunda-2B Discordant SGDP 31,687,839 – 31,824,938 137,098.5 0.00503072 5 66.8073 1,496.8
S_Papuan-14B + S_Korean-1B Discordant SGDP 31,565,428 – 31,805,190 239,762.0 0.00890710 14 116.0858 2,412.0
S_Papuan-14B + S_Pathan-2A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 13 185.2250 1,403.7
S_Papuan-14B + S_Burmese-1B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 13 185.2250 1,403.7
S_Papuan-14B + S_Sindhi-2A Discordant SGDP 31,805,070 – 31,805,190 120.0 0.00000026 2 1.0576 37,821.5
S_Papuan-14B + S_Thai-1A Discordant SGDP 31,792,748 – 31,805,190 12,442.5 0.00133701 2 6.9724 5,736.9
S_Papuan-14B + S_Punjabi-1A Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
S_Papuan-14B + S_Thai-1B Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
S_Papuan-14B + S_Abkhasian-1B Discordant SGDP 31,565,428 – 31,824,938 259,509.5 0.00967891 9 125.5646 1,433.5
S_Papuan-14B + S_Kinh-2B Discordant SGDP 31,805,070 – 31,805,190 120.0 0.00000026 2 1.0576 37,821.5
S_Papuan-14B + S_Bulgarian-1B Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Kinh-1A Discordant SGDP 31,484,549 – 31,805,190 320,641.0 0.02762967 11 154.9077 1,420.2
S_Papuan-14B + S_Czech-2A Discordant SGDP 31,565,428 – 31,805,190 239,762.0 0.00890710 10 116.0858 1,722.9
S_Papuan-14B + S_Dusun-1B Discordant SGDP 31,805,070 – 31,805,190 120.0 0.00000026 2 1.0576 37,821.5
S_Papuan-14B + S_Estonian-2B Discordant SGDP 31,484,549 – 31,824,938 340,388.5 0.02840148 8 164.3865 973.3
S_Papuan-14B + S_Maori-1A Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Finnish-1B Discordant SGDP 31,565,428 – 31,824,938 259,509.5 0.00967891 9 125.5646 1,433.5
S_Papuan-14B + S_Papuan-3A Discordant SGDP 30,953,957 – 31,868,351 914,394.0 0.51304157 89 439.9091 4,046.3
S_Papuan-14B + S_French-1B Discordant SGDP 31,805,070 – 31,820,336 15,266.0 0.00035812 2 8.3277 4,803.3
S_Papuan-14B + S_Papuan-6B Discordant SGDP 31,484,549 – 31,824,938 340,388.5 0.02840148 6 164.3865 730.0
S_Papuan-14B + S_Iranian-2A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 15 185.2250 1,619.7
S_Papuan-14B + S_Papuan-5B Discordant SGDP 31,805,070 – 31,824,938 19,867.5 0.00077207 2 10.5364 3,796.4
S_Papuan-14B + S_Iraqi_Jew-2B Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Papuan-13A Discordant SGDP 31,805,070 – 31,805,190 120.0 0.00000026 2 1.0576 37,821.5
S_Papuan-14B + S_Palestinian-3A Discordant SGDP 31,805,070 – 31,824,938 19,867.5 0.00077207 2 10.5364 3,796.4
S_Papuan-14B + S_Papuan-2B Discordant SGDP 31,792,748 – 31,805,190 12,442.5 0.00133701 2 6.9724 5,736.9
S_Papuan-14B + S_Bergamo-2A Discordant SGDP 31,484,549 – 31,805,190 320,641.0 0.02762967 14 154.9077 1,807.5
S_Papuan-14B + S_Chukchi-1A Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Jordanian-2A Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
S_Papuan-14B + S_Itelman-1B Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
S_Papuan-14B + S_Orcadian-2A Discordant SGDP 31,795,978 – 31,820,336 24,358.5 0.00096379 2 12.6921 3,151.6
S_Papuan-14B + S_Eskimo_Naukan-2A Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
S_Papuan-14B + B_Dai-4A Discordant SGDP 31,484,549 – 31,824,938 340,388.5 0.02840148 15 164.3865 1,825.0
S_Papuan-14B + S_Bengali-2A Discordant SGDP 31,805,070 – 31,820,336 15,266.0 0.00035812 2 8.3277 4,803.3
S_Papuan-14B + B_French-3B Discordant SGDP 31,792,748 – 31,824,938 32,190.0 0.00210881 2 16.4512 2,431.4
S_Papuan-14B + S_Bengali-2B Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Karitiana-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 10 146.4030 1,366.1
S_Papuan-14B + S_Relli-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 12 146.4030 1,639.3
S_Papuan-14B + S_Pima-2B Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
S_Papuan-14B + S_Yadava-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 13 146.4030 1,775.9
B_Papuan-15A + S_Bougainville-1A Discordant SGDP 31,792,748 – 32,353,201 560,453.5 0.43796469 43 270.0177 3,185.0
S_Papuan-14B + S_Mala-3B Discordant SGDP 31,792,748 – 31,868,351 75,603.5 0.00610080 8 37.2897 4,290.7
B_Papuan-15A + S_Papuan-14A Discordant SGDP 31,792,748 – 31,805,190 12,442.5 0.00133701 2 6.9724 5,736.9
S_Papuan-14B + S_Brahmin-1A Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 11 129.1814 1,703.0
B_Papuan-15A + S_Finnish-1A Discordant SGDP 31,792,748 – 31,805,190 12,442.5 0.00133701 2 6.9724 5,736.9
S_Papuan-14B + S_Madiga-1B Discordant SGDP 31,805,070 – 31,820,336 15,266.0 0.00035812 2 8.3277 4,803.3
B_Papuan-15A + S_Polish-1B Discordant SGDP 31,795,978 – 31,824,938 28,960.0 0.00137774 2 14.9008 2,684.4
S_Papuan-14B + S_Madiga-2A Discordant SGDP 31,795,978 – 31,805,190 9,212.5 0.00060593 2 5.4220 7,377.4
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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