NCBI Danio rerio Annotation Release 106

The RefSeq genome records for Danio rerio were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.

The annotation products are available in the sequence databases and on the FTP site.

This report provides:

For more information on the annotation process, please visit the NCBI Eukaryotic Genome Annotation Pipeline page.

Annotation Release information

This annotation should be referred to as NCBI Danio rerio Annotation Release 106

Annotation release ID: 106
Date of Entrez queries for transcripts and proteins: Jun 2 2017
Date of submission of annotation to the public databases: Jun 26 2017
Software version: 7.4


The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
GRCz11GCF_000002035.6Genome Reference Consortium05-09-2017Reference26 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

Counts and length of annotated features are provided below for each assembly.

Feature counts

Primary Assembly
All Alt Loci
Genes and pseudogenes help39,98939,2417,023
  genes with variants11,18710,9601,037
  placed on multiple assembly-units help6,276na909
  with > 5% ab initio help679540139
  with filled gap(s) help772656116
  placed on multiple assembly-units help3,625na564
  known RefSeq (NM_) help15,39315,3783,640
  model RefSeq (XM_)37,42533,0944,331
Other RNAs help17,83215,8302,027
  with > 5% ab initio help000
  with filled gap(s) help1293
  placed on multiple assembly-units help25na6
  known RefSeq (NR_) help45745780
  model RefSeq (XR_) help7,5056,1771,328
  with > 5% ab initio help776611165
  with major correction(s) help743716133
  known RefSeq (NP_) help15,39115,3763,633
  model RefSeq (XP_) help37,42533,0944,331

Detailed reports

Alignment of the annotated proteins to a set of high-quality proteins

The final set of annotated proteins was searched with BLASTP against the UniProtKB/Swiss-Prot curated proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 26110 coding genes, 23570 genes had a protein with an alignment covering 50% or more of the query and 12524 had an alignment covering 95% or more of the query.

Definition of query and target coverage. The query coverage is the percentage of the annotated protein length that is included in the alignment. The target coverage is the percentage of the target length that is included in the alignment.

Below is a cumulative graph displaying the number of genes with alignments above a given query or target coverage threshold. For comparison, corresponding statistics for other organisms annotated by the NCBI eukaryotic annotation pipeline were added to the graph.

Query: annotated proteins
Target: UniProtKB/Swiss-Prot curated proteins

Masking of genomic sequence

Transcript and protein alignments are performed on the repeat-masked genome. Below are the percentages of genomic sequence masked by WindowMasker and RepeatMasker for each assembly. RepeatMasker results are only used for organisms for which a comprehensive repeat library is available.

For this annotation run, transcripts and proteins were aligned to the genome masked with WindowMasker only.
Assembly nameAssembly accession% Masked with RepeatMasker% Masked with WindowMasker

Transcript and protein alignments

The annotation pipeline relies heavily on alignments of experimental evidence for gene prediction. Below are the sets of transcripts and proteins that were retrieved from Entrez, aligned to the genome by Splign or ProSplign and passed to Gnomon, NCBI's gene prediction software.

Depending on the other evidence available, long 454 reads (with average length above 250 nt) may be aligned as traditional evidence and reported in the Transcript alignments section or aligned with RNA-Seq reads and reported in the RNA-Seq alignments section.

Transcript alignments

RefSeq transcript alignment quality report

The known RefSeq transcripts (NM_ and NR_ accessions) are a set of hiqh-quality transcripts maintained by the RefSeq group at NCBI. Alignment statistics for this group of transcripts, such as percent and number of sequences not aligning at all, percent best alignments split between multiple scaffolds, and percent alignments not covering the full CDS are indicative of the genome quality and are provided below.

Primary Assembly
Number of sequences retrieved from Entrez16,155
Number (%) of sequences not aligning35 (0.22%)
Number (%) of sequences with multiple best alignments (split genes)77 (0.48%)
Number (%) of sequences with CDS coverage < 95% help421 (2.69%)

RNA-Seq alignments

The following RNA-Seq reads from the Sequence Read Archive were also used for gene prediction:

  Hide alignments statistics, by sample (SAME, SAMN, SAMD, DRS)
  Show alignments statistics, by run (ERR, SRR, DRR)