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.GFF3 file extension

To open .GFF3 files on Windows, open the file with IGV Desktop by launching IGV and using File > Load from File to select the .gff3.

To open a .gff3 file, use a genome browser/viewer that supports GFF3 (for example, IGV Desktop), or open it as plain text in a code/text editor. If you just need to read it, any text editor works because GFF3 is a tab-delimited text format.

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Last updated: April 30, 2026 · Reviewed by Julian Stricker

Open on your device

Choose your operating system for a dedicated step-by-step opening guide.

How to open .GFF3 files

Use these platform-specific instructions to open .GFF3 files safely.

Windows

  1. Open the file with IGV Desktop by launching IGV and using File > Load from File to select the .gff3.
  2. If you only need to inspect contents, open the .gff3 in a text editor (it is tab-delimited text) and check that columns are separated by tabs.
Full Windows guide

Mac

  1. Open the file with IGV Desktop (File > Load from File) to view the annotations on a genome reference.
  2. For quick inspection or troubleshooting, open the .gff3 in a text/code editor and verify it is tab-delimited with 9 columns per feature line.
Full Mac guide

Linux

  1. Open the file with IGV Desktop (File > Load from File) to visualize features; ensure the file uses the .gff3 extension as expected by IGV.
  2. Alternatively, open in a text editor; Linux desktops may recognize it by its registered MIME type (text/gff3), but it is still plain text.
Full Linux guide

iOS

  1. iOS may not have common, dedicated GFF3 genome browsers; open it as plain text in the Files app (if preview works) or transfer it to a desktop and load it in IGV Desktop for proper visualization.
Full iOS guide

Android

  1. Android may not have common, dedicated GFF3 genome browsers; open it as plain text in a file viewer/editor if needed, or transfer it to a desktop and load it in IGV Desktop for full feature viewing.
Full Android guide

Security notes

  • A .gff3 file is plain text and typically does not contain active content (no macros), but it can still trigger vulnerabilities in poorly implemented parsers—open untrusted files in well-maintained genomics tools.
  • Be cautious with extremely large .gff3 files: they can cause performance issues or crashes in editors/viewers; prefer specialized tools like IGV for large annotation datasets.
  • If a .gff3 file is offered inside an archive or alongside executables/scripts, treat the bundle with caution; the annotation file itself is text, but accompanying files may not be.

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Can't open this file?

These are the most common causes and fixes when .GFF3 files fail to open.

Common reasons

  • The file opens as unreadable or misaligned text
  • IGV (or another viewer) refuses to load the .gff3
  • Features do not appear where expected in a genome browser
  • Upload/import into a service (e.g., Ensembl) fails

Fix steps

  1. Open the file in a code/text editor that preserves tabs and disable word wrap if it makes columns hard to read.
  2. Confirm each feature line has 9 tab-delimited columns (GFF3 structure) and that the attributes appear in the last column.

OS-specific troubleshooting

What is a .GFF3 file?

GFF3 (General Feature Format version 3) is a line-oriented, tab-separated text format where each feature is one line with 9 required columns plus an attributes field. NCBI’s GFF3 follows the Sequence Ontology GFF3 specification and is commonly used for genome annotation exchange and submission workflows.

Background

GFF3 is widely used in genomics and bioinformatics to represent annotations on DNA/RNA sequences—such as genes, transcripts, exons, and coding regions—along genomic coordinates. Each record is a single line, and the file is designed to be both human-readable (as text) and machine-parseable.

In practice, .gff3 files are frequently downloaded from public genome resources (for example, NCBI) or produced by annotation pipelines, then loaded into genome browsers to visualize features aligned to a reference genome. NCBI notes that its GFF3 is formatted according to the Sequence Ontology GFF3 specification, and a compliant 9-column GFF3 can be used for genome annotation-related workflows.

Because it is plain text, a .gff3 file can be inspected and edited in a text editor, but it is best viewed and validated with genomics tools that understand the 9-column structure and attributes (including feature relationships such as Parent/ID used by many tools).

Common MIME types: text/gff3

Further reading

Authoritative resources for more details on the .GFF3 format.

Common .GFF3 issues

The file opens as unreadable or misaligned text

GFF3 relies on tab-separated columns; if your editor displays it with wrapped fields or replaced tabs, it can look corrupted even when it is valid.

  1. Open the file in a code/text editor that preserves tabs and disable word wrap if it makes columns hard to read.
  2. Confirm each feature line has 9 tab-delimited columns (GFF3 structure) and that the attributes appear in the last column.

IGV (or another viewer) refuses to load the .gff3

Viewers typically expect valid GFF3 structure and consistent identifiers/relationships; minor formatting deviations can cause load failures.

  1. Confirm the file uses the .gff3 extension and is formatted as GFF3 (one feature per line, 9 columns, tab-separated).
  2. If the file came from an export or pipeline, re-export or regenerate it as GFF3 conforming to the specification referenced by NCBI/Sequence Ontology.

Features do not appear where expected in a genome browser

Genome browsers require coordinates to match the reference assembly and sequence naming conventions; mismatches can make annotations appear missing.

  1. Verify you loaded the correct reference genome/assembly in the viewer before loading the GFF3 annotations.
  2. Check whether sequence/contig names in column 1 match the reference (for example, chromosome naming differences can prevent mapping).

Upload/import into a service (e.g., Ensembl) fails

Upload tools often enforce specific expectations for GFF3 content and structure beyond basic readability.

  1. Review the service’s GFF3 requirements and ensure your file follows the described structure and conventions.
  2. If needed, simplify the file to core features first (or regenerate from the source) and retry the upload.

FAQ

Is .gff3 just a “document” file?

It is a text-based data/annotation format used in genomics (General Feature Format v3). While it can be read in a text editor, it is primarily meant to be loaded into bioinformatics tools and genome browsers.

What program should I use to view .gff3 as genome annotations?

IGV Desktop supports GFF3 and is commonly used to visualize annotations as tracks against a reference genome.

What does “9-column GFF3” mean?

GFF3 represents each feature as one line with 9 required tab-separated columns (including seqid, type, start/end, and an attributes column). NCBI notes that a 9-column file conforming to the GFF3 specification can be used for genome annotation workflows.

Can I rename another file to .gff3 to convert it?

No. Renaming only changes the extension. The content must actually be in valid GFF3 structure to work in tools that expect GFF3.

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