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NCBI Scatophagus argus Annotation Release 100

The RefSeq genome records for Scatophagus argus 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 Scatophagus argus Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Jan 3 2022
Date of submission of annotation to the public databases: Feb 3 2022
Software version: 9.0

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
fScaArg1.priGCF_020382885.2G10K10-13-2021Reference25 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeaturefScaArg1.pri
Genes and pseudogenes help26,110
  protein-coding22,632
  non-coding3,152
  Transcribed pseudogenes0
  Non-transcribed pseudogenes168
  genes with variants10,905
  Immunoglobulin/T-cell receptor gene segments151
  other7
mRNAs48,205
  fully-supported47,475
  with > 5% ab initio help262
  partial60
  with filled gap(s) help0
  known RefSeq (NM_) help0
  model RefSeq (XM_)48,205
non-coding RNAs help5,391
  fully-supported4,197
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help4,623
pseudo transcripts help0
  fully-supported0
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help0
CDSs48,369
  fully-supported47,475
  with > 5% ab initio help308
  partial69
  with major correction(s) help124
  known RefSeq (NP_) help0
  model RefSeq (XP_) help48,218

Detailed reports

The counts below do not include pseudogenes.

BUSCO analysis of gene annotation

BUSCO v4.1.4 (Simão et al 2015, PMID: 26059717) was run in "protein" mode on the annotated gene set picking one longest protein per gene, and run using the actinopterygii_odb10 lineage dataset. Results are reported for the gene set from the primary assembly unit, and presented in BUSCO notation (C:complete [S:single-copy, D:duplicated], F:fragmented, M:missing, n:number of genes used).

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 22619 coding genes, 21030 genes had a protein with an alignment covering 50% or more of the query and 10321 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 (if calculated), for each assembly. RepeatMasker results are only calculated for organisms with complete Dfam HMM model collections.

For this annotation run, transcripts and proteins were aligned to the genome masked with WindowMasker only.
Assembly nameAssembly accession% Masked with WindowMasker
fScaArg1.priGCF_020382885.220.63%

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, minimap2, or ProSplign and passed to Gnomon, NCBI's gene prediction software.

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)

SRA Long Read Alignment Statistics

The following long read RNA-Seq reads (PacBio, Oxford Nanopore, 454, or other long-read sequencing technologies) from the Sequence Read Archive were also used for gene prediction:

Protein alignments

References