The Genome Variation Map (GVM) is a public data repository of genome variations, including single nucleotide polymorphisms and small insertions and deletions, with particular focuses on human as well as cultivated plants and domesticated animals.
Genome Variations from 27 Species:
SpeciesNCBI Taxonomy ID Assembly Version Number of Variants Project Count Individual Count G2P Pair
SNP INDEL
Animals
Human
Homo sapiens
9606 GRCh37 13,327,822 3,019,815 4 215 180,911
Cattle
Bos taurus
9913 UMD_3.1 53,609,957 6,724,343 9 95 719
Chicken
Gallus gallus
9031 Gallus_gallus-5.0 36,174,851 4,619,064 9 112 1,499
Dog
Canis familiaris
9615 CanFam3.1 18,457,814 - 3 78 532
Duck
Anas platyrhynchos
8839 BGI_duck_1.0 8,213,041 1,484,245 3 3 -
Giant panda
Ailuropoda melanoleuca
9646AilMel1 11,820,056 2,544,981 1 34 -
Goat
Capra hircus
9925 CHIR_2.0 48,505,769 6,389,438 8 233 48
Horse
Equus caballus
9796 EquCab2.0 25,756,212 3,663,455 7 71 -
Killer whale
Orcinus orca
9733Oorca1.1 4,821,960 573,454 1 48 -
Pig
Sus scrofa
9823 Sscrofa10.2 64,709,967 12,087,428 8 247 326
Sheep
Ovis aries
9940 Oar_v4.0  60,025,622 10,395,242 10 125 644
Tarpan
Equus ferus
1114792 EquCab2.0  5,458,905 1,204,691 3 35 -
Plants
Carrot
Daucus carota
79200Dcarota_388_v2.0 21,396,685 5,961,358 2 36 -
Common Bean
Phaseolus vulgaris
3885 Pvulgaris_442_v2.0 13,876,210 3,707,970 6 40 -
Cotton
Gossypium hirsutum
3635 Ghir.BGI 8,665,982 4,170,512 2 391 -
Cucumber
Cucumis sativus
3659B10v2 4,311,436 1,120,282 3 103 -
Date Palm
Phoenix dactylifera
42345DPV02 13,400,840 2,354,618 1 61 -
Grape
Vitis vinifera
29760IGGP_12x 22,527,031 4,175,880 10 50 -
Maize
Zea mays
4577RefGen_v3 1,501,581 - 1 376 3,332
Moso bamboo
Phyllostachys heterocycle
38705 P.heterocycle 1.0 2,009,487 - 1 1 -
Poplar
Populus trichocarpa
3694JGI v3.0 19,861,824 7,727,010 4 926 -
Rice
Oryza sativa
4530IRGSP1.0 18,161,579 - 5 5,152 9,122
Rubber
Hevea brasiliensis
3981 reyan7-33-97 9,584,819 - 1 6 -
Sorghum
Sorghum bicolor
4558Sobic.003G291800 15,413,117 - 3 48 537
Soybean
Glycine max
3847Wm82.a2.v1 19,921,434 3,050,299 8 544 449
Tomato
Solanum lycopersicum
4081 SL2.50 26,938,825 3,724,480 6 579 -
Wheat
Triticum aestivum
4565TGAC v1 1,365,924 114,594 2 62 -
Note: - indicates it is under construction,G2P=Genotype-to-Phenotype
Publications
1. Genome Variation Map: a data repository of genome variations in BIG Data Center. Nucleic Acids Res 2018.[PMID=29069473].
2. The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2017, 45(D1):D18-D24.[PMID=27899658].
3. SorGSD: a sorghum genome SNP database. Biotechnol Biofuels 2016, 9:6. [PMID=26744602].
4. VCGDB: a dynamic genome database of the Chinese population. BMC Genomics 2014, 15:265.[PMID=24708222]
5. DoGSD: the dog and wolf genome SNP database. Nucleic Acids Res 2014, 43(Database issue):D777-783. [PMID=25404132].

Data Submission

Deposit data into GVM

How to cite?

When you have successfully submitted data to GVM, please consider to use the following words to describe data deposition in your manuscript.

The variation data reported in this paper have been deposited in the Genome Variation Map [1] in BIG Data Center [2], Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession number GVMXXXXXX    more>>

News more>>

  •  A total of 537 G2P Pairs derived from Sorghum bicolor (Sorghum) accessions are integrated into GVM (2018-07-12)
  •  A total of 1499 G2P Pairs derived from Gallus gallus (Chicken) accessions are integrated into GVM (2018-07-12)
  •  A total of 13,400,840 SNPs derived from 62 Phoenix dactylifera (Data Palm) accessions are integrated into GVM (2018-07-12)
  •  A total of 22,527,031 SNPs derived from 50 Vitis vinifera (Grape) accessions are integrated into GVM (2018-07-12)
  •  A total of 719 G2P Pairs derived from Bos taurus (Cattle) are integrated into GVM (2018-07-03)
  •  A total of 48 G2P Pairs derived from Capra hircus (Goat) are integrated into GVM (2018-07-03)
  •  A total of 644 G2P Pairs derived from Ovis aries (Sheep) are integrated into GVM (2018-07-03)
  •  A total of 9,122 G2P Pairs derived from Oryza sativa (Rice) are integrated into GVM (2018-07-03)
  •  A total of 25,756,212 SNPs derived from 71 Equus caballus (Horse) accessions are integrated into GVM (2018-06-20)
  •  A total of 5,458,905 SNPs derived from 35 Equus ferus (Tarpan) accessions are integrated into GVM (2018-06-20)
  •  A total of 13,876,210 SNPs derived from 40 Phaseolus vulgaris (Common Bean) accessions are integrated into GVM (2018-06-20)
  •  A total of 8,665,982 SNPs derived from 391 Gossypium hirsutum (Cotton) accessions are integrated into GVM (2018-01-05)
  •  A total of 21,396,685 SNPs derived from 36 Daucus carota (Carrot) accessions are integrated into GVM (2018-01-05)
  •  A total of 4,311,436 SNPs derived from 103 Cucumis sativus (Cucumber) accessions are integrated into GVM (2017-11-20)
  •  GVM is accepted by Nucleic Acids Res at 2017-10-10 (2017-10-19)
  •  A total of 272 G2P Pairs derived from Ovis aries (Sheep) are integrated into GVM (2017-8-10)
  •  A total of 1,249 G2P Pairs derived from Gallus gallus (Chicken) are integrated into GVM (2017-8-04)
  •  A total of 203 G2P Pairs derived from Canis familiaris (Dog) are integrated into GVM (2017-8-02)
  •  A total of 326 G2P Pairs derived from Sus scrofa (Pig) are integrated into GVM (2017-8-02)
  •  A total of 449 G2P Pairs derived from Glycine max (Soybean) are integrated into GVM (2017-8-01)
  •  A total of 60,334,300 SNPs derived from 95 Bos taurus (Cattle) accessions are integrated into GVM (2017-8-01)
  •  A total of 3,332 G2P Pairs derived from Zea mays (Maize) are integrated into GVM (2017-7-23)
  •  A total of 180,911 G2P Pairs derived from Homo sapiens (Human) are integrated into GVM (2017-7-15)
  •  A total of 7,432 G2P Pairs derived from Oryza sativa (Rice) are integrated into GVM (2017-7-05)
  •  A total of 55,763,416 SNPs derived from 125 Ovis aries (Sheep) accessions are integrated into GVM (2017-6-22)
  •  A total of 9,584,819 SNPs derived from 6 Hevea brasiliensis (Rubber) accessions are integrated into GVM (2017-6-22)
  •  A total of 19,861,824 SNPs derived from 926 Populus trichocarpa (Poplor) accessions are integrated into GVM (2017-6-22)
  •  A total of 36,174,851 SNPs derived from 112 Gallus gallus (Chicken) accessions are integrated into GVM (2017-5-31)
  •  A total of 19,921,434 SNPs derived from 544 Glycine max (Soybean) accessions are integrated into GVM (2017-5-31)
  •  A total of 1,365,924 SNPs derived from 62 Triticum aestivum (Wheat) accessions are integrated into GVM (2017-5-31)
  •  A total of 4,821,960 SNPs derived from 48 Orcinus orca (Killer whale) accessions are integrated into GVM (2017-5-31)
  •  A total of 2,009,487 SNPs derived from 5 Phyllostachys heterocycle (Mobo bamboos) accessions are integrated into GVM (2017-5-31)
  •  A total of 13,327,822 SNPs derived from 215 Homo sapiens (human) accessions are integrated into GVM (2017-3-31)
  •  A total of 4,821,960 SNPs derived from 48 Orcinus Orca (whale) accessions are integrated into GVM (2017-3-31)
  •  A total of 11,820,056 SNPs derived from 34 ailuropoda melanoleuca (panda) accessions are integrated into GVM (2017-3-31)
  •  A total of 1,501,581 SNPs derived from 376 Zea mays accessions are integrated into GVM (2016-9-18)
  •  A total of 18,161,579 SNPs derived from 5152 rice accessions are integrated into RVD (2016-6-18)
  •  A total of 77 individual dog samples are included in DoGSD (2016-6-12)
  •  The Genome Variation Map is publicly available online (2016-6-10)

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Species-specific Variations

Rice Variation Database
Sorghum Genome SNP Database
Dog Genome SNP Database
Virtual Chinese Genome Database

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