Download variation files or useful tools in GVM

Variation Data

All genomic variation data are publicly available. Variation data files in VCF and FASTA formats 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.
 
Organism (version) SNP (VCF) SNP (VCF) SNP (FASTA) Short INDEL (VCF) Short INDEL (VCF) Short INDEL (FASTA)
Anas platyrhynchos (BGI_duck_1.0) Brief VCF Detailed VCF FASTA
Anopheles gambiae (AgamP3) Brief VCF Detailed VCF FASTA
Apis mellifera (Amel_4.5) Brief VCF Detailed VCF FASTA
Arabidopsis thaliana (TAIR10) Brief VCF Detailed VCF FASTA
Aspergillus fumigatus (ASM265v1) Brief VCF Detailed VCF FASTA
Astyanax mexicanus (Astyanax_mexicanus-1.0.2) Brief VCF Detailed VCF FASTA
Bos indicus (Bos_indicus_1.0) Brief VCF Detailed VCF FASTA
Bos indicus x Bos taurus (Btau_3.1) Brief VCF Detailed VCF FASTA
Bos taurus (Bos_taurus_UMD_3.1.1) Brief VCF Detailed VCF FASTA
Brassica napus (Brassica_napus_assembly_v1.0) Brief VCF Detailed VCF FASTA
Brassica oleracea (BOL) Brief VCF Detailed VCF FASTA
Brassica rapa (Brapa_1.0) Brief VCF Detailed VCF FASTA
Caenorhabditis elegans (WS195) Brief VCF Detailed VCF FASTA
Callithrix jacchus (Callithrix_jacchus-3.2) Brief VCF Detailed VCF FASTA
Canis lupus familiaris (CanFam3.1) Brief VCF Detailed VCF FASTA
Capra aegagrus (CHIR_1.0) Brief VCF Detailed VCF FASTA
Capra hircus (CHIR_1.0) Brief VCF Detailed VCF FASTA
Capsicum annuum (Pepper_Zunla_1_Ref_v1.0) Brief VCF Detailed VCF FASTA
Chlorocebus sabaeus (Chlorocebus_sabeus_1.1) Brief VCF Detailed VCF FASTA
Cicer arietinum (ASM33114v1) Brief VCF Detailed VCF FASTA
Ciona intestinalis (KH) Brief VCF Detailed VCF FASTA
Clupea harengus (ASM96633v1) Brief VCF Detailed VCF FASTA
Coturnix japonica (Coturnix_japonica_2.0) Brief VCF Detailed VCF FASTA
Danio rerio (Zv9) Brief VCF Detailed VCF FASTA
Daucus carota subsp. sativus (ASM162521v1) Brief VCF Detailed VCF FASTA
Drosophila melanogaster (Release_6_plus_ISO1_MT) Brief VCF Detailed VCF FASTA
Elaeis guineensis (EG5) Brief VCF Detailed VCF FASTA
Equus caballus (EquCab2.0) Brief VCF Detailed VCF FASTA
Felis catus (Felis_catus_8.0) Brief VCF Detailed VCF FASTA
Ficedula albicollis (FicAlb1.5) Brief VCF Detailed VCF FASTA
Gallus gallus (Gallus_gallus-5.0) Brief VCF Detailed VCF FASTA
Glycine max (Glycine_max_v2.0) Brief VCF Detailed VCF FASTA
Gorilla gorilla (gorGor3.1) Brief VCF Detailed VCF FASTA
Gossypium hirsutum (ASM98774v1) Brief VCF Detailed VCF FASTA
Macaca fascicularis (Macaca_fascicularis_5.0) Brief VCF Detailed VCF FASTA
Macaca mulatta (Mmul_8.0.1) Brief VCF Detailed VCF FASTA
Malus domestica (MalDomGD1.0) Brief VCF Detailed VCF FASTA
Medicago truncatula (MedtrA17_3.5) Brief VCF Detailed VCF FASTA
Meleagris gallopavo (Turkey_5.0) Brief VCF Detailed VCF FASTA
Microtus ochrogaster (MicOch1.0) Brief VCF Detailed VCF FASTA
Monodelphis domestica (MonDom5) Brief VCF Detailed VCF FASTA
Mus musculus (GRCm38.p4) Brief VCF Detailed VCF FASTA
Nomascus leucogenys (Nleu_3.0) Brief VCF Detailed VCF FASTA
Nothobranchius furzeri (Nfu_20140520) Brief VCF Detailed VCF FASTA
Oreochromis niloticus (Orenil1.1) Brief VCF Detailed VCF FASTA
Ornithorhynchus anatinus (Ornithorhynchus_anatinus_5.0.1) Brief VCF Detailed VCF FASTA
Oryctolagus cuniculus (OryCun2.0) Brief VCF Detailed VCF FASTA
Oryza sativa (IRGSP-1.0) Brief VCF Detailed VCF FASTA
Ovis aries (Oar_v4.0) Brief VCF Detailed VCF FASTA
Ovis orientalis (Oar_v3.1) Brief VCF Detailed VCF FASTA
Pan troglodytes (Pan_tro 3.0) Brief VCF Detailed VCF FASTA
Parus major (Parus_major1.0.3) Brief VCF Detailed VCF FASTA
Phoenix dactylifera (DPV01) Brief VCF Detailed VCF FASTA
Pongo abelii (P_pygmaeus_2.0.2) Brief VCF Detailed VCF FASTA
Populus trichocarpa (Poptr1_1) Brief VCF Detailed VCF FASTA
Rattus norvegicus (Rnor_6.0) Brief VCF Detailed VCF FASTA
Salmo salar (ICSASG_v2) Brief VCF Detailed VCF FASTA
Solanum lycopersicum (SL2.50) Brief VCF Detailed VCF FASTA
Sorghum bicolor (Sorbi1) Brief VCF Detailed VCF FASTA
Sus scrofa (Sscrofa11.1) Brief VCF Detailed VCF FASTA
Taeniopygia guttata (Taeniopygia_guttata-3.2.4) Brief VCF Detailed VCF FASTA
Tribolium castaneum (Tcas5.2) Brief VCF Detailed VCF FASTA
Vitis vinifera (12X) Brief VCF Detailed VCF FASTA
Zea mays (B73_RefGen_v3) Brief VCF Detailed VCF FASTA

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:
2. Genome alignment tools:
3. Variants annotation tools: