NCBI Pundamilia nyererei Annotation Release 101

The RefSeq genome records for Pundamilia nyererei 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 Pundamilia nyererei Annotation Release 101

Annotation release ID: 101
Date of Entrez queries for transcripts and proteins: Aug 28 2015
Date of submission of annotation to the public databases: Aug 31 2015
Software version: 6.4

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
PunNye1.0GCF_000239375.1Broad Institute12-22-2011Referenceunplaced scaffolds

Gene and feature statistics

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

Feature counts

FeaturePunNye1.0
Genes and pseudogenes help24,222
  protein-coding22,960
  non-coding1,006
  pseudogenes256
  genes with variants7,599
mRNAs38,583
  fully-supported34,867
  with > 5% ab initio help1,551
  partial892
  with filled gap(s) help0
  known RefSeq (NM_) help2
  model RefSeq (XM_)38,581
Other RNAs help1,906
  fully-supported1,418
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help1,418
CDSs38,653
  fully-supported34,867
  with > 5% ab initio help1,758
  partial901
  with major correction(s) help156
  known RefSeq (NP_) help2
  model RefSeq (XP_) help38,581

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 22890 coding genes, 21354 genes had a protein with an alignment covering 50% or more of the query and 10269 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
PunNye1.0GCF_000239375.12.75%20.20%

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

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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