Genome Variation Map (GVM; Version 2.0) is a data portal of genomic variations, including single nucleotide polymorphisms (SNP) and small insertions & deletions, with particular focuses on domesticated plants and animials, Chinese population and other resource species of China.
        GVM is open-access and public available for worldwide scientific communities. Users could query all variants by variant effect, gene name, chromosome location, trait ontology, study project, etc. and download interested data for further study.
There are currently 18 species variations in GVM v2.0:
SpeciesTaxonomy ID Assembly Ver. Short Variants Projects No. Individuals No. Assocaition Phenotype
SNP Number Indel Number
Rice
Oryza sativa
4530IRGSP1.0 18,161,579   5 5152 Y
Maize
Zea mays
4577RefGen_v3 1,501,581   1 376 Y
Sorghum
Sorghum bicolor
4558Sorbi3 15,513,117   2 48 NA
Wheat
Triticum aestivum
4565TGAC v1 1,365,924 114,594 1 0 NA
Soybean
Glycine max
3847Wm82.a2.v1 19,921,434 3,050,299 8 544 NA
Tomato
Solanum lycopersicum
4081 SL2.50     6? ? NA
Goat
Capra hircus
9925 CHIR_2.0 8 234 NA
Dog
Canis familiaris
9615 CanFam3.1 18,457,814   3 78 NA
Pig
Sus scrofa
9823 Sscrofa10.2 8 270 NA
Chicken
Gallus gallus
9031 Gallus_gallus-5.0 36,174,851 4,619,064 9 112 NA
Sheep
Ovis aries
9940 Oar_v4.1  10 126 NA
Duck
Anas platyrhynchos
8839 BGI_duck_1.0 3 3 NA
Poplor
Populus trichocarpa
3694JGI v3.0 19,861,824 7,727,010 4 926 NA
Bamboos
Phyllostachys heterocycle
4581 P.heterocycle 1.0 2,009,487 0 1 0 NA
Killer whales
Orcinus orca
9733Oorca1.1 4,821,960
573,454 1 48 NA
Giant panda
Ailuropoda melanoleuca
9646AilMel1 11,820,056
2,544,981 1 34 NA
Rubber
Hevea brasiliensis
3981 reyan7-33-97 9,584,819
1 6 NA
Human
Homo sapiens
9606 GRCh37 13,327,822
3,019,815 4 215 Y
Publication
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].

Online Submission

Deposit data into GVM

News

  •  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

Related Links

NCBI Variation
    dbSNP
    dbVar
    dbGaP

EBI Variation
    EVA
    DGVa
    EGA

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