NCBI Xenopus (Silurana) tropicalis Annotation Release 102

The RefSeq genome records for Xenopus (Silurana) tropicalis 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 Xenopus (Silurana) tropicalis Annotation Release 102

Annotation release ID: 102
Date of Entrez queries for transcripts and proteins: Jun 19 2015
Date of submission of annotation to the public databases: Jun 23 2015
Software version: 6.3

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
Xtropicalis_v7GCF_000004195.2DOE Joint Genome Institute12-19-2012Reference1 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureXtropicalis_v7
Genes and pseudogenes help25,222
  protein-coding22,229
  non-coding2,591
  pseudogenes402
  genes with variants8,076
mRNAs40,258
  fully-supported37,002
  with > 5% ab initio help1,957
  partial2,125
  with filled gap(s) help185
  known RefSeq (NM_) help8,379
  model RefSeq (XM_)31,879
Other RNAs help6,603
  fully-supported3,920
  with > 5% ab initio help0
  partial21
  with filled gap(s) help20
  known RefSeq (NR_) help188
  model RefSeq (XR_) help3,732
CDSs40,322
  fully-supported37,002
  with > 5% ab initio help2,115
  partial1,723
  with major correction(s) help873
  known RefSeq (NP_) help8,366
  model RefSeq (XP_) help31,879

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 22139 coding genes, 20215 genes had a protein with an alignment covering 50% or more of the query and 12219 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
Xtropicalis_v7GCF_000004195.232.69%36.85%

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.

Xtropicalis_v7
Primary Assembly
Number of sequences retrieved from Entrez8,779
Number (%) of sequences not aligning132 (1.50%)
Number (%) of sequences with multiple best alignments (split genes)178 (2.06%)
Number (%) of sequences with CDS coverage < 95% help726 (8.59%)

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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