NCBI Taeniopygia guttata Annotation Release 103

The RefSeq genome records for Taeniopygia guttata 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 Taeniopygia guttata Annotation Release 103

Annotation release ID: 103
Date of Entrez queries for transcripts and proteins: May 19 2015
Date of submission of annotation to the public databases: May 26 2015
Software version: 6.3

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
Taeniopygia_guttata-3.2.4GCF_000151805.1Washington University Genome Sequencing Center02-08-2013Reference36 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureTaeniopygia_guttata-3.2.4
Genes and pseudogenes help17,713
  protein-coding16,371
  non-coding1,190
  pseudogenes152
  genes with variants1,778
mRNAs19,437
  fully-supported11,767
  with > 5% ab initio help4,271
  partial2,906
  with filled gap(s) help198
  known RefSeq (NM_) help869
  model RefSeq (XM_)18,568
Other RNAs help1,630
  fully-supported1,291
  with > 5% ab initio help0
  partial10
  with filled gap(s) help9
  known RefSeq (NR_) help248
  model RefSeq (XR_) help1,043
CDSs19,439
  fully-supported11,767
  with > 5% ab initio help4,899
  partial2,736
  with major correction(s) help1,802
  known RefSeq (NP_) help862
  model RefSeq (XP_) help18,568

Detailed reports

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 16355 coding genes, 15918 genes had a protein with an alignment covering 50% or more of the query and 10362 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
Taeniopygia_guttata-3.2.4GCF_000151805.17.83%19.54%

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 short reads and reported in the Short read transcript 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.

Taeniopygia_guttata-3.2.4
Primary Assembly
Number of sequences retrieved from Entrez1,250
Number (%) of sequences not aligning39 (3.12%)
Number (%) of sequences with multiple best alignments (split genes)9 (0.74%)
Number (%) of sequences with CDS coverage < 95% help240 (24.92%)

Short read transcript alignments

The following short reads (RNA-Seq) 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

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