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NCBI Branchiostoma floridae Annotation Release 100

The RefSeq genome records for Branchiostoma floridae 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 Branchiostoma floridae Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Aug 11 2020
Date of submission of annotation to the public databases: Aug 13 2020
Software version: 8.5

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
Bfl_VNyyKGCF_000003815.2DOE Joint Genome Institute04-29-2020Reference20 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureBfl_VNyyK
Genes and pseudogenes help29,857
  protein-coding26,689
  non-coding3,042
  transcribed pseudogenes3
  non-transcribed pseudogenes123
  genes with variants6,676
  immunoglobulin/T-cell receptor gene segments0
  other0
mRNAs43,028
  fully-supported35,985
  with > 5% ab initio help4,024
  partial1,399
  with filled gap(s) help1,147
  known RefSeq (NM_) help0
  model RefSeq (XM_)43,028
non-coding RNAs help3,977
  fully-supported3,364
  with > 5% ab initio help0
  partial1
  with filled gap(s) help1
  known RefSeq (NR_) help0
  model RefSeq (XR_) help3,536
pseudo transcripts help3
  fully-supported1
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help3
CDSs43,041
  fully-supported35,985
  with > 5% ab initio help4,409
  partial1,258
  with major correction(s) help821
  known RefSeq (NP_) help13
  model RefSeq (XP_) help43,028

Detailed reports

The counts below do not include pseudogenes.

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 26676 coding genes, 18839 genes had a protein with an alignment covering 50% or more of the query and 4014 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
Bfl_VNyyKGCF_000003815.214.63%24.05%

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

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