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section		 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
Yanjin Black-bone chicken Southern East Asia Jan 1,2021 FTP
Yellow-feather Black-bone chicken Southern East Asia Jan 1,2021 FTP
Yeonsan Ogye Northern East Asia Jan 1,2021 FTP
Yugan Black-bone chicken Southern East Asia Jan 1,2021 FTP
Yulin chicken Southern East Asia Jan 1,2021 FTP
Yunyang Black-bone chicken Northern East Asia Jan 1,2021 FTP
Zhangzhou Game chicken Southern East Asia Jan 1,2021 FTP
Zhengyang Yellow chicken Northern East Asia Jan 1,2021 FTP
Zhuxiang chicken Southern East Asia Jan 1,2021 FTP
Zombori kaporka Europe 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

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