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:
X2131765159
Alleles:
reference
A
–
alternate
C
–
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Chromosome 10   position  31,765,159  (GRCh37)
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 98.1%
1.9%
EAS 98.9%
1.1%
OCN 100.0%
0.0%
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 C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP406.1 generations 98  =  1  +  971.000
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_Yi-2A + S_Kyrgyz-1B Concordant SGDP 31,068,515 – 32,453,881 1,385,366.0 0.86991083 14 665.9757 420.4
S_Kyrgyz-1B + S_Tubalar-2A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_Mixtec-2A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Piapoco-1B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Kyrgyz-1B + S_Karitiana-2A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_Iraqi_Jew-1B Discordant SGDP 31,765,104 – 31,795,978 30,874.0 0.00116764 3 15.8195 3,792.8
S_Kyrgyz-1B + S_Burusho-2B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_Papuan-14B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 14 146.4030 1,912.5
S_Yi-2A + S_Even-3A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Ulchi-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 11 146.4030 1,502.7
S_Yi-2A + S_Ulchi-2A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Tubalar-1A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 3 14.2691 4,204.9
S_Yi-2A + S_Tubalar-2A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Quechua-1A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Quechua-2A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Kyrgyz-1B + S_Cambodian-2B Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 11 129.1814 1,703.0
S_Kyrgyz-1B + S_Yi-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 9 146.4030 1,229.5
S_Yi-2A + S_Yakut-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 13 146.4030 1,775.9
S_Kyrgyz-1B + S_Madiga-2A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Tlingit-2A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Kyrgyz-1B + S_Bulgarian-1A Discordant SGDP 31,765,104 – 31,824,938 59,834.0 0.00254537 4 29.7203 2,691.8
S_Yi-2A + S_Tu-2B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + B_Papuan-15B Discordant SGDP 31,765,104 – 31,824,938 59,834.0 0.00254537 3 29.7203 2,018.8
S_Yi-2A + S_Uygur-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 15 146.4030 2,049.1
S_Yi-2A + B_French-3A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Tujia-1B Discordant SGDP 31,092,468 – 31,792,748 700,280.0 0.30017584 48 337.1344 2,847.5
S_Yi-2A + S_Pima-2B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Dai-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 13 146.4030 1,775.9
S_Kyrgyz-1B + S_Quechua-3B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Uygur-2B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_Tubalar-1A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 3 14.2691 4,204.9
S_Yi-2A + S_She-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 5 146.4030 683.0
S_Kyrgyz-1B + S_Miao-1B Discordant SGDP 31,565,543 – 31,868,351 302,808.0 0.01341798 15 146.3478 2,049.9
S_Yi-2A + S_Tu-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 15 146.4030 2,049.1
S_Kyrgyz-1B + S_Papuan-5B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Korean-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 13 146.4030 1,775.9
S_Kyrgyz-1B + S_Mala-2B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Korean-1A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_Kusunda-2A Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 9 83.2118 2,163.2
S_Yi-2A + S_Burmese-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 11 146.4030 1,502.7
S_Kyrgyz-1B + S_Abkhasian-1B Discordant SGDP 31,134,695 – 31,795,978 661,282.5 0.24516534 53 318.4156 3,329.0
S_Yi-2A + S_Thai-1A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Kyrgyz-1B + S_Saami-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 11 146.4030 1,502.7
S_Yi-2A + S_Kinh-2B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Kyrgyz-1B + S_Bergamo-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 12 146.4030 1,639.3
S_Yi-2A + S_Maori-1B Discordant SGDP 31,765,104 – 31,868,351 103,247.5 0.00653736 7 50.5588 2,769.1
S_Kyrgyz-1B + S_Surui-1A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Papuan-3B Discordant SGDP 31,765,104 – 31,824,938 59,834.0 0.00254537 3 29.7203 2,018.8
S_Yi-2A + S_Zapotec-1B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Papuan-14A Discordant SGDP 31,765,104 – 31,795,978 30,874.0 0.00116764 3 15.8195 3,792.8
S_Yi-2A + S_Karitiana-1A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Papuan-2A Discordant SGDP 31,034,032 – 31,868,351 834,319.5 0.38828804 55 401.4734 2,739.9
S_Yi-2A + S_Piapoco-2A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Chukchi-1B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Mayan-1A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Itelman-1B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_Zapotec-2B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Mala-3B Discordant SGDP 31,765,104 – 31,868,351 103,247.5 0.00653736 8 50.5588 3,164.6
S_Kyrgyz-1B + S_Quechua-2A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Brahmin-1A Discordant SGDP 31,765,104 – 31,868,351 103,247.5 0.00653736 4 50.5588 1,582.3
S_Kyrgyz-1B + S_Altaian-1A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Kusunda-2B Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 9 83.2118 2,163.2
S_Kyrgyz-1B + S_Yakut-2B Discordant SGDP 31,727,319 – 31,868,351 141,032.0 0.00809458 3 68.6954 873.4
S_Yi-2A + S_Punjabi-4A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 13 146.4030 1,775.9
S_Kyrgyz-1B + S_Naxi-3B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Czech-2B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_Han-1A Discordant SGDP 31,765,104 – 31,824,938 59,834.0 0.00254537 3 29.7203 2,018.8
S_Yi-2A + S_English-2A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_Kinh-1A Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 12 129.1814 1,857.9
S_Yi-2A + S_Estonian-2B Discordant SGDP 31,565,428 – 32,403,755 838,326.5 0.46873980 78 403.3967 3,867.2
S_Kyrgyz-1B + S_Papuan-4A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Estonian-1A Discordant SGDP 31,565,428 – 31,792,748 227,319.5 0.00757009 10 110.1134 1,816.3
S_Kyrgyz-1B + S_Papuan-9A Discordant SGDP 31,765,104 – 31,795,978 30,874.0 0.00116764 3 15.8195 3,792.8
S_Yi-2A + S_Finnish-2B Discordant SGDP 31,565,428 – 31,792,748 227,319.5 0.00757009 10 110.1134 1,816.3
S_Kyrgyz-1B + S_Madiga-1B Discordant SGDP 31,765,104 – 31,795,978 30,874.0 0.00116764 3 15.8195 3,792.8
S_Yi-2A + S_Finnish-1B Discordant SGDP 31,565,428 – 31,795,978 230,549.5 0.00830117 9 111.6638 1,612.0
S_Kyrgyz-1B + S_Kusunda-1A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Yi-2A + S_Iraqi_Jew-2B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Kyrgyz-1B + S_Pathan-2B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Palestinian-3A Discordant SGDP 31,765,104 – 31,824,938 59,834.0 0.00254537 4 29.7203 2,691.8
S_Kyrgyz-1B + S_Kalash-2A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Sardinian-1B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_Albanian-1B Discordant SGDP 31,565,428 – 31,795,978 230,549.5 0.00830117 11 111.6638 1,970.2
S_Yi-2A + S_Jordanian-2A Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_English-1B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Jordanian-1B Discordant SGDP 31,765,104 – 31,820,336 55,232.5 0.00213143 3 27.5116 2,180.9
S_Kyrgyz-1B + S_Hungarian-2A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Norwegian-1B Discordant SGDP 31,765,104 – 31,792,748 27,644.0 0.00043656 2 14.2691 2,803.3
S_Kyrgyz-1B + S_Bergamo-1A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Orcadian-1A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Kyrgyz-1B + B_Dai-4B Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 69 353.1549 3,907.6
S_Yi-2A + S_Orcadian-2B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Kyrgyz-1B + S_Chane-1B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Polish-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 9 146.4030 1,229.5
S_Kyrgyz-1B + S_Karitiana-1A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + S_Russian-1B Discordant SGDP 31,565,428 – 31,792,748 227,319.5 0.00757009 9 110.1134 1,634.7
S_Kyrgyz-1B + S_Piapoco-1A Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
S_Yi-2A + B_Crete-1B Discordant SGDP 31,765,104 – 31,765,215 111.0 0.00000015 2 1.0533 37,976.6
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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