GFF3 File Format - Definition and supported options
The GFF (General Feature Format) format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines. The following documentation is based on the Version 3 specifications.
The first line of a GFF3 file must be a comment that identifies the version, e.g.
Fields must be tab-separated. Also, all but the final field in each feature line must contain a value; "empty" columns should be denoted with a '.'
- seqid - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seq ID must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID, without any additional content such as species or assembly. See the example GFF output below.
- source - name of the program that generated this feature, or the data source (database or project name)
- type - type of feature. Must be a term or accession from the SOFA sequence ontology
- start - Start position of the feature, with sequence numbering starting at 1.
- end - End position of the feature, with sequence numbering starting at 1.
- score - A floating point value.
- strand - defined as + (forward) or - (reverse).
- phase - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..
- attributes - A semicolon-separated list of tag-value pairs, providing additional information about each feature. Some of these tags are predefined, e.g. ID, Name, Alias, Parent - see the GFF documentation for more details.
Note that where the attributes contain Parent identifiers, these will be used by Ensembl to display the features as joined blocks.
##gff-version 3 ctg123 . mRNA 1300 9000 . + . ID=mrna0001;Name=sonichedgehog ctg123 . exon 1300 1500 . + . ID=exon00001;Parent=mrna0001 ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mrna0001 ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mrna0001 ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mrna0001 ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mrna0001
For more information about this file format, see the documentation on the GMOD wiki.