Genome Variation Map

Download variation files or useful tools in GVM

Variation Data

All genomic variation data on this page are publicly available. Variation data in VCF and FASTA formats, VEP annotation in TEXT format, and population variant after phasing in VCF format are tabulated as below.

Note:
   Brief VCF is the vcf format file without individual genotype;
   Detailed VCF is the vcf format file with individual genotype.
   FASTA is the flank sequence of variant site in FASTA format.
   VEP Annotation is the consequence annotation of variant site.
   Phased VCF is variation data after filtering and phasing.

Organism (version)	SNP (VCF)	SNP (VCF)	SNP (FASTA)	Short INDEL (VCF)	Short INDEL (VCF)	Short INDEL (FASTA)	VEP annotation	Phased VCF
Ailuropoda melanoleuca (AilMel1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Ailuropoda melanoleuca (ASM200744v2)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Ailurus fulgens (ASM200746v1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Anas platyrhynchos (BGI_duck_1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Anser cygnoides (PRJNA183603_v1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Bos mutus (BosGru_v2.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Bos taurus (UMD_3.1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Brassica napus (Bra_napus_v2.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Brassica rapa (CAAS_Brap_v3.01)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Callithrix jacchus (mCalJac1.pat.X)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Canis familiaris (CanFam3.1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Cannabis sativa (GCF_900626175.1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Capra hircus (CHIR_2.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Capsicum annuum (Zunla 1 Ref_v1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Catharanthus roseus (ASM94934v1.1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Cenchrus americanus (GCA_947561735.1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Cucumis melo (USDA_Cmelo_AY_1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Cucumis sativus (B10v2)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Daucus carota (Dcarota_388_v2.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Equus caballus (EquCab2.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Equus ferus (EquCab2.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Fagopyrum tataricum (Pinku1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Felis catus (Felis_catus_9.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Gallus gallus (Gallus_gallus-5.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Ganoderma lucidum (GanLuc1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Glycine max (Wm82.a2.v1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Gossypium hirsutum (Ghir.BGI)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Hevea brasiliensis (reyan7-33-97)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Homo sapiens (GRCh37)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Hordeum vulgare (MorexV2)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Human coronavirus 229E (NC_002645.1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Human coronavirus HKU1 (NC_006577.2)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Human coronavirus NL63 (NC_005831.2)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Human coronavirus OC43 (NC_006213.1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Ipomoea batatas (pasi3)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Jatropha curcas (JatCur_1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Juglans regia (Jregia_v1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Macaca fascicularis (Macaca_fascicularis_6.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Macaca mulatta (Mmul_10)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Manihot esculenta (Manihot esculenta v6.1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Manis javanica (YNU_ManJav_2.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
MERS-CoV (NC_019843.3)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Monkeypox virus (ON563414.3)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Orcinus orca (Oorca1.1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Oryza sativa (IRGSP1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Ovis aries (Oar_v4.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Pan troglodytes (Pan_tro_3.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Panicum miliaceum (Longmi4)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Papio anubis (Panubis1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Phaseolus vulgaris (Pvulgaris_442_v2.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Phoenix dactylifera (DPV02)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Phyllostachys heterocycla (P.heterocycle 1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Populus trichocarpa (JGI v3.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Prunus mume (P.mume_V1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Ricinus communis (ASM1957865v1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Saccharum spontaneum (Np-X)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Salvia miltiorrhiza (Salvia_genome)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
SARS-CoV (NC_004718.3)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Setaria italica (Xiaomi V1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Setaria italica (Setaria_italica_v2.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Solanum lycopersicum (SL2.50)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Solanum tuberosum (v6.1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Sorghum bicolor (Sorbi3)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Sus scrofa (Sscrofa10.2)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Triticum aestivum (IWGSC1.0)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Triticum aestivum (TGAC v1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Triticum urartu (IGDB v1)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Vigna radiata (Vrad_JL7)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Vitis vinifera (IGGP_12x)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF
Zea mays (RefGen_v4)	Brief VCF	Detailed VCF	FASTA	Brief VCF	Detailed VCF	FASTA	VEP	Phased VCF

About the data

VCF (Variant Call Format) is a simplified text file format containing information about a position in the genome. More details about its format and specifications are listed below.

1. #CHROM is short for chromosome number
2. POS is short for chromosome position
3. ID is variation identifier in GVM system
4. REF is short for reference allele
5. ALT is short for alternate allele
6. QUAL is variants quality
7. FILTER is filter status
8. INFO is additional information for each variant

More detail information of vcf. format can be found in http://samtools.github.io/hts-specs/VCFv4.1.pdf

FASTA format provide 50nt flanking sequences for each variants (50nt for each flank) which is typically useful for BLAST applications. e.g.

>OSA01S123 class=1|alleles="A/G"|version=1
AGGTCCAGGCTGCCAAGCTTGAACTCCGTCTCCCAGACGACGACGGCCGC
R
GGAGGAAGGCGGACCATGTCGCCGGTGAGGTTGTTGCAGACAGACACGCA

Useful tools

1. Variants calling tools:

Genome Analysis Toolkit (GATK): https://www.broadinstitute.org/gatk/
Picard: http://www.psc.edu/index.php/user-resources/software/picard
samtools and bcftools: http://samtools.sourceforge.net/

2. Genome alignment tools:

Bwa: http://bio-bwa.sourceforge.net/

3. Variants annotation tools:

Vep: http://www.ensembl.org/info/docs/tools/vep/index.html