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Reference Genome VCF files BAM files FASTQ files

Reference Genome

The chicken reference genome GRCg6a (INSDC Assembly GCA_000002315.5) is used in the current version of Chicken2K. The sequence and annotation of GRCg6a are accessible in Ensembl and NCBI. The versions used in Chicken2K can also be downloaded from our FTP.

Items Sample Version Release date Download
DNA sequence (FASTA) Red Jungle Fowl(UCD001)#256 GRCg6a (GCA_000002315.5) March 27,2018 FTP
GRCg6a.99.chr(GTF) Red Jungle Fowl(UCD001)#256 Gallus_gallus.GRCg6a.99.chr March 27,2018 FTP

VCF files

The following list provides the links to several individual breeds. The links can be used to download the data directly. Use the search and filter function of the header to quickly find the target file.

Population Region Release date Download
Ceylon Jungle Fowl Ceylon Jungle Fowl Jan 1,2021 FTP
Chigulu chicken Southern East Asia Jan 1,2021 FTP
Cochin Europe Jan 1,2021 FTP
Combatiente Europe Jan 1,2021 FTP
Cornish Europe Jan 1,2021 FTP
Cream Legbar Europe Jan 1,2021 FTP
Crevecour Europe Jan 1,2021 FTP
Croad Langshan Europe Jan 1,2021 FTP
Dagu chicken Northern East Asia Jan 1,2021 FTP
Daweishan Mini chicken Southern East Asia Jan 1,2021 FTP
Dehua Black chicken Southern East Asia Jan 1,2021 FTP
Derbyshire Redcap Europe Jan 1,2021 FTP
Dongxiang Blue-eggshell chicken Southern East Asia Jan 1,2021 FTP
Dorking Europe Jan 1,2021 FTP
Dulong chicken Southern East Asia Jan 1,2021 FTP
Emei Black chicken Southern East Asia Jan 1,2021 FTP
English Maran Europe Jan 1,2021 FTP
Ethiopia Native chicken Africa Jan 1,2021 FTP
Faverolle Europe Jan 1,2021 FTP
Fayoumi Africa Jan 1,2021 FTP

BAM files

The following list provides downloading links to 1,986 samples. Use the search function to sort certain individual with ID or population with population name. It is recommended to download BAM files via GSA with project number PRJCA002606.

FASTQ files

The following list provides downloading links to 1,986 samples. Use the search function to sort certain individual with ID or population with population name. It is recommended to download FASTQ files via Ensembl, NCBI, and GSA with the corresponding access numbers. Especially, some FASTQ files are accessible in ChickenSD