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Data released on April 25, 2014

Genomic

Genomic data of the American Crow (Corvus brachyrhynchos).

Zhang, G; Li,B ; Li,C ; Gilbert,T; Jarvis,E; The Avian Genome Consortium; Wang,J (2014): Genomic data of the American Crow (Corvus brachyrhynchos). GigaScience Database. http://dx.doi.org/10.5524/101008 RIS BibTeX Text

The American Crow (Corvus brachyrhynchos brachyrhynchos (Brehm, 1822)) is a large passerine bird and part of the Corvidae family. It is commonly found throughout North America, and despite being common and widespread, they are highly susceptible to West Nile Virus.
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a female in the Asheboro, North Carolina Zoo, USA, with blood samples provided by Halley Buckanoff of the zoo. We sequenced the 1.26Gb genome to a depth of approximately 80X with short reads from a series of libraries with various insert sizes (170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb).
The assembled scaffolds of high quality sequences total 1.1Gb, with the contig and scaffold N50 values of 24kb and 6.9Mb respectively. We identified 16,562 protein-coding genes with a mean length of 17.9kb.

Related datasets:

doi:10.5524/101008 IsSupplementTo doi:10.5524/101000

Accessions (data included in GigaDB):

BioProject: PRJNA212867
SRA: SRP028286

Projects:

The Avian Phylogenomic Project

Samples:

Sample ID Taxonomic ID Common name Genbank name Scientific name Sample attributes
American crow-10-0582 85066 American Crow American Crow Corvus brachyrhynchos short_name="CORBR"
BioMaterial_ref="Erich Jarvis "
funding_source="BGI"
sample_source=""
source material identifiers="CBH11DN01"
est_genome_size="1.26"
ploidy="diploid"
tissue_type="UBERON:0000178(blood)"
geographic location (country and/or sea,region)="USA, North Carolina, Asheboro"
geographic location (latitude and longitude)="not recorded"
sex="F"
IUNC_Red_List="LC"
Sample_contact="Halley Buckanoff - Ashboro NC Zoo"

Files (FTP site) (Aspera):Aspera user name: gigadb , password: gigadb Table Settings
Items per page:

File Name Sample ID File Type File Format Size Release Date

Corvus_brachyrhynchos.cds.gz

American crow-10-0582 Coding sequence FASTA 2 7 71244116.79 MB 2014-04-25

Corvus_brachyrhynchos.fa.gz

American crow-10-0582 Genome assembly FASTA 2 9 327298238312.14 MB 2014-04-25

Corvus_brachyrhynchos.gff.gz

American crow-10-0582 Annotation GFF 2 7 17719811.69 MB 2014-04-25

Corvus_brachyrhynchos.pep.gz

American crow-10-0582 Protein sequence FASTA 2 7 46368734.42 MB 2014-04-25

Corvus_brachyrhynchos.RepeatMasker.out.gz

American crow-10-0582 other UNKNOWN 2 7 97716539.32 MB 2014-04-25