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NCBI Lepisosteus oculatus Annotation Release 101

The RefSeq genome records for Lepisosteus oculatus 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 Lepisosteus oculatus Annotation Release 101

Annotation release ID: 101
Date of Entrez queries for transcripts and proteins: Jan 6 2016
Date of submission of annotation to the public databases: Jan 8 2016
Software version: 6.5

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
LepOcu1GCF_000242695.1Broad Institute01-13-2012Reference30 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureLepOcu1
Genes and pseudogenes help21,445
  protein-coding18,843
  non-coding2,485
  pseudogenes117
  genes with variants8,686
mRNAs41,634
  fully-supported38,798
  with > 5% ab initio help838
  partial561
  with filled gap(s) help0
  known RefSeq (NM_) help2
  model RefSeq (XM_)41,632
Other RNAs help4,534
  fully-supported4,047
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help4,047
CDSs41,706
  fully-supported38,798
  with > 5% ab initio help1,104
  partial564
  with major correction(s) help199
  known RefSeq (NP_) help2
  model RefSeq (XP_) help41,632

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 18771 coding genes, 17581 genes had a protein with an alignment covering 50% or more of the query and 9469 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
LepOcu1GCF_000242695.10.94%22.32%

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

Comparison of the current and previous annotations

The annotation produced for this release (101) was compared to the annotation in the previous release (100) 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.

LepOcu1 (Current) to LepOcu1 (Previous)
Identical help1%
Minor changes help34%
Major changes help43%
New help22%
Deprecated help2%
Other help<1%
Download the reporttabular, Genome Workbench

References

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