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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
Scots Grey Europe Jan 1,2021 FTP
Sentul chicken Southeast Asia Jan 1,2021 FTP
Serama chicken Southeast Asia Jan 1,2021 FTP
Shandong Yuanbao chicken Northern East Asia Jan 1,2021 FTP
Shimian Caoke chicken Southern East Asia Jan 1,2021 FTP
Shouguang chicken Northern East Asia Jan 1,2021 FTP
Silkies Southern East Asia Jan 1,2021 FTP
Southern Xinjiang Game chicken Northern East Asia Jan 1,2021 FTP
Spanish Europe Jan 1,2021 FTP
Speckled Sussex Europe Jan 1,2021 FTP
Sri Lanka Game chicken South Asia Jan 1,2021 FTP
Sri Lanka Native chicken South Asia Jan 1,2021 FTP
Sumatra chicken Southeast Asia Jan 1,2021 FTP
Surena Europe Jan 1,2021 FTP
Taiwan Native chicken Southern East Asia Jan 1,2021 FTP
Tajikistan Game chicken Central Asia Jan 1,2021 FTP
Tajikistan Native chicken Central Asia Jan 1,2021 FTP
Thailand Gama chicken Southeast Asia Jan 1,2021 FTP
Thailand Native chicken Southeast Asia Jan 1,2021 FTP
Tianfu Black-bone chicken Southern East 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