NCBI Nematostella vectensis Annotation Release 100

The RefSeq genome records for Nematostella vectensis 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 Nematostella vectensis Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Jan 29 2020
Date of submission of annotation to the public databases: Feb 9 2020
Software version: 8.3

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
ASM20922v1GCF_000209225.1DOE Joint Genome Institute (JGI)08-22-2007Referenceunplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureASM20922v1
Genes and pseudogenes help37,751
  protein-coding23,845
  non-coding13,293
  transcribed pseudogenes17
  non-transcribed pseudogenes596
  genes with variants5,894
  immunoglobulin/T-cell receptor gene segments0
  other0
mRNAs34,311
  fully-supported30,698
  with > 5% ab initio help2,156
  partial4,181
  with filled gap(s) help2,846
  known RefSeq (NM_) help0
  model RefSeq (XM_)34,311
non-coding RNAs help14,674
  fully-supported6,200
  with > 5% ab initio help0
  partial16
  with filled gap(s) help14
  known RefSeq (NR_) help0
  model RefSeq (XR_) help7,469
pseudo transcripts help19
  fully-supported16
  with > 5% ab initio help0
  partial0
  with filled gap(s) help1
  known RefSeq (NR_) help0
  model RefSeq (XR_) help19
CDSs34,311
  fully-supported30,698
  with > 5% ab initio help2,340
  partial3,921
  with major correction(s) help1,608
  known RefSeq (NP_) help0
  model RefSeq (XP_) help34,311

Detailed reports

The counts below do not include pseudogenes.

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 23845 coding genes, 16058 genes had a protein with an alignment covering 50% or more of the query and 3403 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
ASM20922v1GCF_000209225.123.43%23.99%

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

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)

Protein alignments

Comparison of the current and previous annotations

The annotation produced for this release (100) was compared to the annotation in the previous release for each assembly annotated in both releases. Scores for current and previous gene and transcript features were calculated based on overlap in exon sequence and matches in exon boundaries. Pairs of current and previous features were categorized based on these scores, whether they are reciprocal best matches, and changes in attributes (gene biotype, completeness, etc.). If the assembly was updated between the two releases, alignments between the current and the previous assembly were used to match the current and previous gene and transcript features in mapped regions.

The table below summarizes the changes in the gene set for each assembly as a percent of the number of genes in the current annotation release, and provides links to the details of the comparison in tabular format and in a Genome Workbench project.

ASM20922v1 (Current) to ASM20922v1 (Previous)
Identical help<1%
Minor changes help19%
Major changes help26%
New help53%
Deprecated help26%
Other help1%
Download the reporttabular, Genome Workbench

References

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