Chicken Genome Data Repository
Data Repository
Name Size Time Last Modified
Chicken600K_Ensembl_76_vep.txt.gz 13.33 MB2015-02-05 19:07:59
Chicken_60K_allResults.txt.gz 3.69 MB2013-01-18 12:32:45
Chicken_60K_allResults.xlsx.gz 5.55 MB2013-01-18 11:47:28
Chicken_60K_info.txt.gz 4.36 MB2011-03-21 09:06:43
Chicken_60K_tabl.txt.gz 1.62 MB2011-03-21 09:07:24
GGA5_HISAT2Index 9 files2018-04-26 14:50:35
Genome_annotations 105 files2016-09-10 22:01:06
ISU_Trinity.fa.gz 33.46 MB2011-10-28 15:07:28
Multisites_contigs_unigenes.xlsx.gz 15.1 MB2012-01-27 18:54:50
UCDavis.Zhou 4 files2017-09-11 18:56:28
The NAGRP Data Repository: 125 data files at this location
Data sources/credits:

o Chicken_60K_allResults.xlsx.gz
o Chicken_60K_allResults.txt.gz
  - From
  - Data: Flanking sequences and mapping info on build v.2, 2.1, and 4.
  - Data format:
      Column A:  SNP ID  
      Column B:  Flanking seq    
      Column C:  Chr      (galGal3 build 2.0)    
      Column D:  Position (galGal3 build 2.0)    
      Column E:  Chr      (galGal3 build 2.1)    
      Column F:  Position (galGal3 build 2.1)    
      Column G:  Chr      (galGal4)  
      Column H:  Position (galGal4)
      Column I-L: Additional (duplicated) mapping info.

o Chicken600K_Ensembl_vep.txt.gz
  -- Ensembl VEP annotated chicken 600K SNP chip data

o Chicken_60K_info.txt.gz
  - 60K chip SNPs with flanking sequences
  - Genome location information (build 2)

o Chicken_60K_tabl.txt.gz
  - All 350K Illumina seq. identified SNPs and their dbSNP numbers
  - Ref: Martien AM Groenen, Hendrik-Jan Megens, Yalda Zare,
    Wesley C Warren, LaDeana W Hillier, Richard PMA Crooijmans, Addie
    Vereijken, Ron Okimoto, William Muir and Hans H Cheng. The
    development and characterization of a 60K SNP chip for chicken.
    BMC Genomics 2011, 12:274 (31 May 2011) []

o Genome_Build
  - GFF files of the genome assembly

o ISU_Trinity.fa.gz
  - Chicken spleen EST sequences by Solexa deep sequencing.

o Multisites_contigs_unigenes.xlsx
  - Posted by Qinghua Nie (

o UCDavis.Zhou
  - Private collaboration folder

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