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NCBI Pyrgilauda ruficollis Annotation Release 100

The RefSeq genome records for Pyrgilauda ruficollis 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 Pyrgilauda ruficollis Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: May 4 2021
Date of submission of annotation to the public databases: May 6 2021
Software version: 8.6

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
ASM1759013v1GCF_017590135.1Institute of Zoology, Chinese Academy of Sciences03-26-2021Reference1 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureASM1759013v1
Genes and pseudogenes help17,565
  protein-coding16,034
  non-coding1,396
  Transcribed pseudogenes6
  Non-transcribed pseudogenes87
  genes with variants6,446
  Immunoglobulin/T-cell receptor gene segments42
  other0
mRNAs32,619
  fully-supported30,473
  with > 5% ab initio help956
  partial886
  with filled gap(s) help0
  known RefSeq (NM_) help0
  model RefSeq (XM_)32,619
non-coding RNAs help2,980
  fully-supported2,499
  with > 5% ab initio help0
  partial1
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help2,743
pseudo transcripts help6
  fully-supported4
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help6
CDSs32,674
  fully-supported30,473
  with > 5% ab initio help1,145
  partial908
  with major correction(s) help486
  known RefSeq (NP_) help0
  model RefSeq (XP_) help32,632

Detailed reports

The counts below do not include pseudogenes.

BUSCO analysis of gene annotation

BUSCO v4.0.2 (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 passeriformes_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 16021 coding genes, 15603 genes had a protein with an alignment covering 50% or more of the query and 10546 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
ASM1759013v1GCF_017590135.118.93%

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)

Protein alignments

References