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NCBI Ovis aries Annotation Release GCF_016772045.2-RS_2023_10

The genome sequence records for Ovis aries RefSeq assembly GCF_016772045.2 (ARS-UI_Ramb_v3.0) 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_016772045.2-RS_2023_10".

Date of Entrez queries for transcripts and proteins: Oct 17 2023
Date of submission of annotation to the public databases: Oct 30 2023
Software version: 10.2

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
ARS-UI_Ramb_v3.0GCF_016772045.2University of Idaho07-20-2023Reference29 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureARS-UI_Ramb_v3.0
Genes and pseudogenes help35,057
  protein-coding21,300
  non-coding9,697
  Transcribed pseudogenes8
  Non-transcribed pseudogenes3,813
  genes with variants12,872
  Immunoglobulin/T-cell receptor gene segments209
  other30
mRNAs76,688
  fully-supported75,490
  with > 5% ab initio help612
  partial162
  with filled gap(s) help0
  known RefSeq (NM_) help889
  model RefSeq (XM_)75,799
non-coding RNAs help15,488
  fully-supported11,261
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help106
  model RefSeq (XR_) help12,876
pseudo transcripts help8
  fully-supported7
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help1
  model RefSeq (XR_) help7
CDSs76,910
  fully-supported75,490
  with > 5% ab initio help731
  partial130
  with major correction(s) help739
  known RefSeq (NP_) help902
  model RefSeq (XP_) help75,799

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 21287 coding genes, 20890 genes had a protein with an alignment covering 50% or more of the query and 18252 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
ARS-UI_Ramb_v3.0GCF_016772045.240.07%

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:

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.

ARS-UI_Ramb_v3.0
Primary Assembly
Number of sequences retrieved from Entrez1,023
Number (%) of sequences not aligning1 (0.10%)
Number (%) of sequences with multiple best alignments (split genes)0 (0.00%)
Number (%) of sequences with CDS coverage < 95% help4 (0.44%)

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)

CAGE alignments

The following CAGE 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 alignments of the following long RNA-Seq reads (PacBio, Oxford Nanopore, 454, or other long-read sequencing technologies) from the Sequence Read Archive with minimap2 were used for gene prediction:

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
ARS-UI_Ramb_v3.0 (Current) Coverage: 99.02%ARS-UI_Ramb_v3.0 (Current) Coverage: 99.32%
ARS-UI_Ramb_v2.0 (Previous) Coverage: 100.00%ARS-UI_Ramb_v2.0 (Previous) Coverage: 100.00%
Percent Identity: 100.00%Percent Identity: 99.99%

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.

ARS-UI_Ramb_v3.0 (Current) to ARS-UI_Ramb_v2.0 (Previous)
Identical help36%
Minor changes help46%
Major changes help9%
New help9%
Deprecated help5%
Other help<1%
Download the reporttabular, Genome Workbench

References