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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
Ancona Europe Jan 1,2021 FTP
Aijiao chicken Southern East Asia Jan 1,2021 FTP
America Commercial Broiler North America Jan 1,2021 FTP
Andalusian Europe Jan 1,2021 FTP
Anyi Gray chicken Southern East Asia Jan 1,2021 FTP
Appenzeller Europe Jan 1,2021 FTP
Aseel South Asia Jan 1,2021 FTP
Balinese Game chicken Southeast Asia Jan 1,2021 FTP
Banati Kopamnyaka Europe Jan 1,2021 FTP
Beijing You chicken Northern East Asia Jan 1,2021 FTP
Bengal Native chicken South Asia Jan 1,2021 FTP
Bian chicken Northern East Asia Jan 1,2021 FTP
Black Java North America Jan 1,2021 FTP
Black Maltese Europe Jan 1,2021 FTP
Black Sumatra North America Jan 1,2021 FTP
Brahma North America Jan 1,2021 FTP
Bresse Gauloise Europe Jan 1,2021 FTP
Brown Leghorn Europe Jan 1,2021 FTP
Campine Europe Jan 1,2021 FTP
Cemani chicken Southeast 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