NCBI Ictalurus punctatus Annotation Release 100

The RefSeq genome records for Ictalurus punctatus 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 Ictalurus punctatus Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Jul 1 2016
Date of submission of annotation to the public databases: Jul 6 2016
Software version: 7.1

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
IpCoco_1.2GCF_001660625.1Auburn University06-21-2016Reference30 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureIpCoco_1.2
Genes and pseudogenes help27,788
  protein-coding23,218
  non-coding4,177
  pseudogenes393
  genes with variants11,174
mRNAs47,961
  fully-supported46,923
  with > 5% ab initio help310
  partial1,524
  with filled gap(s) help1,158
  known RefSeq (NM_) help1,221
  model RefSeq (XM_)46,740
Other RNAs help6,578
  fully-supported5,933
  with > 5% ab initio help0
  partial16
  with filled gap(s) help16
  known RefSeq (NR_) help0
  model RefSeq (XR_) help5,933
CDSs48,183
  fully-supported46,923
  with > 5% ab initio help381
  partial1,157
  with major correction(s) help534
  known RefSeq (NP_) help1,221
  model RefSeq (XP_) help46,740

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 22996 coding genes, 21290 genes had a protein with an alignment covering 50% or more of the query and 11142 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
IpCoco_1.2GCF_001660625.15.66%33.12%

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

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.

IpCoco_1.2
Primary Assembly
Number of sequences retrieved from Entrez1,286
Number (%) of sequences not aligning31 (2.41%)
Number (%) of sequences with multiple best alignments (split genes)6 (0.48%)
Number (%) of sequences with CDS coverage < 95% help26 (2.07%)

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

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