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NCBI Physeter catodon Annotation Release GCF_002837175.3-RS_2023_04

The genome sequence records for Physeter catodon RefSeq assembly GCF_002837175.3 (ASM283717v5) were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies.

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 "GCF_002837175.3-RS_2023_04".

Date of Entrez queries for transcripts and proteins: Apr 5 2023
Date of submission of annotation to the public databases: Apr 14 2023
Software version: 10.1

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
ASM283717v5GCF_002837175.3BGI02-28-2023Reference22 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureASM283717v5
Genes and pseudogenes help29,662
  protein-coding20,411
  non-coding5,837
  Transcribed pseudogenes22
  Non-transcribed pseudogenes3,321
  genes with variants10,231
  Immunoglobulin/T-cell receptor gene segments43
  other28
mRNAs51,723
  fully-supported49,170
  with > 5% ab initio help1,223
  partial655
  with filled gap(s) help0
  known RefSeq (NM_) help11
  model RefSeq (XM_)51,712
non-coding RNAs help11,892
  fully-supported9,204
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help10,869
pseudo transcripts help22
  fully-supported18
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help22
CDSs51,779
  fully-supported49,170
  with > 5% ab initio help1,462
  partial658
  with major correction(s) help1,813
  known RefSeq (NP_) help24
  model RefSeq (XP_) help51,712

Detailed reports

The counts below do not include pseudogenes.

BUSCO analysis of gene annotation

BUSCO v4.1.4 was run in "protein" mode on the annotated gene set picking one longest protein per gene, and run using the cetartiodactyla_odb10 lineage dataset. Results are reported for the gene set from the primary assembly unit, and presented in BUSCO notation.

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 20398 coding genes, 20015 genes had a protein with an alignment covering 50% or more of the query and 16293 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
ASM283717v5GCF_002837175.332.43%

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 Nucleotide, Entrez Protein, and SRA, and aligned to the genome.

Transcript alignments

The alignments of the following transcripts with Splign were used for gene prediction:

RNA-Seq alignments

The alignments of the following RNA-Seq reads with STAR 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

The alignments of the following proteins with ProSplign were used for gene prediction:

Assembly-assembly alignments of current to previous assembly

When the assembly changes between two rounds of annotation, genes in the current and the previous annotation are mapped to each other using the genomic alignments of the current assembly to the previous assembly so that gene identifiers can be preserved. The success of the remapping depends largely on how well the two assembly versions align to each other.

Below are the percent coverage of one assembly by the other and the average percent identity of the alignments. The 'First pass' alignments are reciprocal best hits, while the 'Total' alignments also include 'Second pass' or non-reciprocal best alignments. For more information about the assembly-assembly alignment process, please visit the NCBI Genome Remapping Service page.

First PassTotal
ASM283717v5 (Current) Coverage: 100.00%ASM283717v5 (Current) Coverage: 100.00%
ASM283717v2 (Previous) Coverage: 99.28%ASM283717v2 (Previous) Coverage: 99.31%
Percent Identity: 99.80%Percent Identity: 99.79%

Comparison of the current and previous annotations

The annotations produced for this release were compared to the annotations 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.

ASM283717v5 (Current) to ASM283717v2 (Previous)
Identical help31%
Minor changes help53%
Major changes help10%
New help5%
Deprecated help8%
Other help<1%
Download the reporttabular, Genome Workbench

References

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