what is the '.' , '+' means in GTF file

Question

[bxia]

I see there are two columns after start and end, but can't find what does them mean?

Is that for strand +/-? then what is '.' means?

Thanks

Answer 1

[WouterDeCoster]

Fields

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 '.'

seqname - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seqname 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) feature - feature type name, e.g. Gene, Variation, Similarity 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). frame - 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.. attribute - A semicolon-separated list of tag-value pairs, providing additional information about each feature.

From: http://www.ensembl.org/info/website/upload/gff.html#fields

Answer 2

[SES]

The columns after the start/end are the score and the strand. The GFF3 file specification is on github now. For the strand, if there is a '.' and not '+' or '-' it means the feature is not stranded.