NCBI Bombyx mori Annotation Release 102

The RefSeq genome records for Bombyx mori 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 Bombyx mori Annotation Release 102

Annotation release ID: 102
Date of Entrez queries for transcripts and proteins: May 30 2017
Date of submission of annotation to the public databases: Jun 6 2017
Software version: 7.4

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
ASM15162v1GCF_000151625.1The international silkworm genome sequencing consortium04-28-2008Reference1 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureASM15162v1
Genes and pseudogenes help16,378
  protein-coding13,798
  non-coding2,490
  pseudogenes90
  genes with variants4,339
mRNAs22,504
  fully-supported21,230
  with > 5% ab initio help638
  partial2,270
  with filled gap(s) help1,388
  known RefSeq (NM_) help2,317
  model RefSeq (XM_)20,187
Other RNAs help3,332
  fully-supported2,795
  with > 5% ab initio help0
  partial18
  with filled gap(s) help18
  known RefSeq (NR_) help417
  model RefSeq (XR_) help2,385
CDSs22,497
  fully-supported21,230
  with > 5% ab initio help695
  partial1,839
  with major correction(s) help1,235
  known RefSeq (NP_) help2,310
  model RefSeq (XP_) help20,187

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 Drosophila melanogaster known RefSeq proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 13791 coding genes, 10167 genes had a protein with an alignment covering 50% or more of the query and 3060 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: Drosophila melanogaster known RefSeq 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
ASM15162v1GCF_000151625.122.17%41.42%

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.

ASM15162v1
Primary Assembly
Number of sequences retrieved from Entrez2,808
Number (%) of sequences not aligning6 (0.21%)
Number (%) of sequences with multiple best alignments (split genes)85 (3.03%)
Number (%) of sequences with CDS coverage < 95% help204 (8.56%)

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

Comparison of the current and previous annotations

The annotation produced for this release (102) was compared to the annotation in the previous release (101) 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.

ASM15162v1 (Current) to ASM15162v1 (Previous)
Identical help16%
Minor changes help60%
Major changes help10%
New help11%
Deprecated help5%
Other help3%
Download the reporttabular, Genome Workbench

References

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