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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
Nigeria Game chicken Africa Jan 1,2021 FTP
Nigeria Native chicken Africa Jan 1,2021 FTP
Ningdu Yellow chicken Southern East Asia Jan 1,2021 FTP
Nixi chicken Southern East Asia Jan 1,2021 FTP
Nunukan chicken Southeast Asia Jan 1,2021 FTP
Olagan Southeast Asia Jan 1,2021 FTP
Old English Pheasant Fowl Europe Jan 1,2021 FTP
Onagadori Northern East Asia Jan 1,2021 FTP
Orpington Europe Jan 1,2021 FTP
Pakistan Native chicken South Asia Jan 1,2021 FTP
Penedesenca Europe Jan 1,2021 FTP
Pengxian Yellow chicken Southern East Asia Jan 1,2021 FTP
Peru Game Fowl South America Jan 1,2021 FTP
Pita Pinta Asturiana Europe Jan 1,2021 FTP
Poland Europe Jan 1,2021 FTP
Qingyuan Partridge chicken Southern East Asia Jan 1,2021 FTP
Red Jungle Fowl Red Jungle Fowl Jan 1,2021 FTP
Rhode Lsland Red chicken North America Jan 1,2021 FTP
Romagnola Europe Jan 1,2021 FTP
Saudi Arabia chicken Western Asia 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