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 19 Species:
SpeciesNCBI Taxonomy ID Assembly Version Number of Variants Project Count Individual Count G2P Pair
SNP INDEL
Cattle
Bos taurus
9913 UMD_3.1 53,609,957 6,724,343 9 95 -
Chicken
Gallus gallus
9031 Gallus_gallus-5.0 36,174,851 4,619,064 9 112 1,249
Dog
Canis familiaris
9615 CanFam3.1 18,457,814 - 3 78 203
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 -
Human
Homo sapiens
9606 GRCh37 13,327,822 3,019,815 4 215 180,911
Killer whale
Orcinus orca
9733Oorca1.1 4,821,960 573,454 1 48 -
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 -
Pig
Sus scrofa
9823 Sscrofa10.2 64,709,967 12,087,428 8 247 326
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 7,432
Rubber
Hevea brasiliensis
3981 reyan7-33-97 9,584,819 - 1 6 -
Sheep
Ovis aries
9940 Oar_v4.0  60,025,622 10,395,242 10 125 272
Sorghum
Sorghum bicolor
4558Sorbi3 15,513,117 - 3 48 -
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. The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2017, 45(D1):D18-D24.[PMID=27899658].
2. VCGDB: a dynamic genome database of the Chinese population. BMC Genomics 2014, 15:265.[PMID=24708222]
3. DoGSD: the dog and wolf genome SNP database. Nucleic Acids Res 2014, 43(Database issue):D777-783. [PMID=25404132].
4. SorGSD: a sorghum genome SNP database. Biotechnol Biofuels 2016, 9:6. [PMID=26744602].

Data Submission

Deposit data into GVM

News

  •  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)

Species-specific Variations

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

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