When annotating an assembly, the NCBI Eukaryotic Genome Annotation Pipeline staff select sequence reads from several RNA-Seq studies and generate read alignments on the assembly. The pipeline uses these alignments as evidence for individual genes and their splice variants. The NCBI staff further include the alignments in sequence and genome data viewers where you can use them to examine the evidence for the transcript of your interest or access tissue-specific gene expression. To learn about the origin of the aligned reads, use the annotation reports (AR) for current annotation releases.
Two ways to access annotation reports are:
- (1) From individual gene records in the Gene database:
- Use the Full Report (default) display of a gene record (example).
- Access the Genomic context section of the record (located below the Summary section)
- Click on the Annotation release number in the first column of the tabular display to access the annotation report.
- (2) From the Genome homepage:
- Select the Eukaryotic Genome Annotation link that is located under the Genome Annotation and Analysis listing.
- On the resulting page, link to all genomes annotated by the NCBI Eukaryotic Genome Annotation Pipeline.
- Locate the genome of your interest and use the AR link in the table to access the annotation report.
Once you access a report (example: the human annotation report for annotation release 108):
- Select the Transcript and protein alignments link (from the table of contents located at the top of the page)
- In the Transcript and protein alignments section (example) select the RNA-Seq alignments link
- The RNA-Seq alignments section (example) provides:
- a listing of the samples that contributed the reads by their BioSample database accession numbers (example SAMEA2142680)
- a listing of other related identifiers (SRA accessions) accessible through the Show alignment statistics by run (ERR, SRR, DRR) link that is located under the samples table