NCBI Rhinopithecus bieti Annotation Release 100

The RefSeq genome records for Rhinopithecus bieti 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 Rhinopithecus bieti Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Aug 18 2016
Date of submission of annotation to the public databases: Aug 25 2016
Software version: 7.1

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
ASM169854v1GCF_001698545.1Laboratory for conservation and utilization of Bio-resource08-03-2016Reference1 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureASM169854v1
Genes and pseudogenes help33,174
  protein-coding21,831
  non-coding5,133
  pseudogenes6,210
  genes with variants9,851
mRNAs49,582
  fully-supported46,807
  with > 5% ab initio help1,030
  partial1,282
  with filled gap(s) help0
  known RefSeq (NM_) help0
  model RefSeq (XM_)49,582
Other RNAs help8,770
  fully-supported8,378
  with > 5% ab initio help0
  partial3
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help8,381
CDSs49,766
  fully-supported46,807
  with > 5% ab initio help1,307
  partial1,289
  with major correction(s) help3,377
  known RefSeq (NP_) help0
  model RefSeq (XP_) help49,582

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 21647 coding genes, 20919 genes had a protein with an alignment covering 50% or more of the query and 17423 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 RepeatMasker only.
Assembly nameAssembly accession% Masked with RepeatMasker% Masked with WindowMasker
ASM169854v1GCF_001698545.147.60%33.74%

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 RNA-Seq reads and reported in the RNA-Seq alignments section.

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

Support Center