Genomics Facilities

The Variation Database

The NARF variation database is comprised of two databases: a single nucleotide polymorphism (SNP) database, and an Insertion/Deletion (InDel) database. The SNP database contains genotyping information for 8 inbred lines that are currently maintained by NARF.The InDel database contains Insertion/Deletion polymorphism data for 4 lines currently maintained by NARF.

You can search the two database by following the links below.

This database has been built using the Chicken Genome and uses the Variant Coordinates in Assembly Galgal 4.


Further information on the Variation data can be found in the papers referenced below:

"Functional classification of 15 million SNPs detected from diverse chicken populations",
AA Gheyas, C Boschiero, L Eory, H Ralph, R Kuo, JA Woolliams, and DW Burt,
DNA Research, Vol. 22, No. 3, pp. 205-217, 2015.

"Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes",
C Boschiero, AA Gheyas, HK Ralph, L Eory L, B Paton, R Kuo, J Fulton, R Preisinger, P Kaiser and DW Burt,
BMC Genomics, Vol. 16, No. 1, pp. 1-17, 2015.

Avian Genomes on Avianbase

The Avianbase Project is an initiative led by the Roslin Institute in collaboration with the Avian Phylogenomics Consortium and Ensembl to make the initial sequence and annotation available for 47 bird species within the Ensembl framework.

The genome sequences, except for budgerigar and bald eagle, were sequenced by the BGI. Genome annotations were also generated by BGI using GeneWise based on a selection of Ensembl transcripts for chicken, zebra finch and human. For completeness we also provide links to the Ensembl genome browser for the following 47 bird species


Further information on the Avianbase data and annotation can be found in the paper referenced below:

"Avianbase: a community resource for bird genomics",
L Eöry, MT Gilbert, C Li, B Li, A Archibald, BL Aken, G Zhang, E Jarvis, P Flicek and DW Burt,
Genome Biology Vol.16, No.21, pp.1--4, 2015.

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