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  • meaning of gff3 file score

    I got a gff3 file, in column 6 (score column), most of them are ".", but some has number such as 18.3465 or 19.1278

    What are those number mean? I did not find clear answer by searching online.

    Thanks.

  • #2
    See here: http://www.sequenceontology.org/gff3.shtml You may have to figure out what exactly is in your GFF file.

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    • #3
      Are those in the 6th column? If so, they're a score for whatever feature they're associated with (maybe E-values?).

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      • #4
        I actually inherited it from other group...

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        • #5
          Since it seems that it's not obvious from context (file name, other annotations, etc.), the best you can do is track down whomever made it and ask.

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          • #6
            There may be something in the 9th column that tells you about the score. The attributes can have notes to say something about the annotation or there may be specific tags that indicates what type of feature this is. I agree with the other comments though, the best case scenario is to find out about this file from the source. I know that is not always possible, so it is always good to try and understand the data as best as possible.

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