NCBI Gallus gallus Annotation Release 104

The RefSeq genome records for Gallus gallus 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 Gallus gallus Annotation Release 104

Annotation release ID: 104
Date of Entrez queries for transcripts and proteins: Apr 13 2018
Date of submission of annotation to the public databases: May 17 2018
Software version: 8.0

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
GRCg6aGCF_000002315.5Genome Reference Consortium03-27-2018Reference35 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureGRCg6a
Genes and pseudogenes help24,373
  protein-coding17,477
  non-coding6,534
  transcribed pseudogenes22
  non-transcribed pseudogenes240
  genes with variants10,544
  immunoglobulin/T-cell receptor gene segments99
  other1
mRNAs49,661
  fully-supported48,584
  with > 5% ab initio help513
  partial564
  with filled gap(s) help16
  known RefSeq (NM_) help6,401
  model RefSeq (XM_)43,260
non-coding RNAs help13,087
  fully-supported12,105
  with > 5% ab initio help0
  partial2
  with filled gap(s) help0
  known RefSeq (NR_) help771
  model RefSeq (XR_) help11,700
pseudo transcripts help28
  fully-supported26
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help5
  model RefSeq (XR_) help23
CDSs49,772
  fully-supported48,584
  with > 5% ab initio help654
  partial369
  with major correction(s) help673
  known RefSeq (NP_) help6,413
  model RefSeq (XP_) help43,260

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 17464 coding genes, 16383 genes had a protein with an alignment covering 50% or more of the query and 11286 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
GRCg6aGCF_000002315.512.52%20.37%

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.

GRCg6a
Primary Assembly
Number of sequences retrieved from Entrez7,248
Number (%) of sequences not aligning26 (0.36%)
Number (%) of sequences with multiple best alignments (split genes)17 (0.24%)
Number (%) of sequences with CDS coverage < 95% help50 (0.78%)

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

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
GRCg6a (Current) Coverage: 97.77%GRCg6a (Current) Coverage: 98.38%
Gallus_gallus-5.0 (Previous) Coverage: 84.70%Gallus_gallus-5.0 (Previous) Coverage: 93.04%
Percent Identity: 99.86%Percent Identity: 99.57%

Comparison of the current and previous annotations

The annotation produced for this release (104) was compared to the annotation in the previous release (103) 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.

GRCg6a (Current) to Gallus_gallus-5.0 (Previous)
Identical help16%
Minor changes help56%
Major changes help11%
New help14%
Deprecated help24%
Other help2%
Download the reporttabular, Genome Workbench

References

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