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Blue tit assembly and gene annotation

Assembly

The cyaCae2 assembly was submitted by Dr. Bernd Tmmermann, NGS core facility, MPI Molecular Genetics on January 2018. The assembly is on scaffold level, consisting of 50,541 contigs assembled into 29,297 scaffolds. From these sequences, 31 chromosomes have been built. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 105,778 while the scaffold N50 is 16,846,143.

Gene annotation

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblycyaCae2, INSDC Assembly GCA_002901205.1, Jan 2018
Base Pairs1,186,980,630
Golden Path Length1,186,980,630
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2018
Genebuild releasedApr 2019
Genebuild last updated/patchedMar 2020
Database version100.2

Gene counts

Coding genes15,470
Non coding genes8,955
Small non coding genes437
Long non coding genes8,343
Misc non coding genes175
Pseudogenes84
Gene transcripts41,815

Other

Genscan gene predictions46,205

About this species

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