Apologies, I didn't look carefully enough at the file I attached. The file type numbers from February 2015 are below, and we should have a current list for you soon.
Since we don't currently publish this anywhere, not sure how you would cite this other than to say that the stats were provided by Dryad.
5, Open Document Format Spreadsheet
2655, Comma-separated values (CSV)
2, Tex/LateX document
2987, Microsoft Excel OpenXML
2522, Unknown data format
10, Microsoft PowerPoint OpenXML
4, Microsoft Powerpoint 97-2007
2040, Microsoft Excel 97-2007
32, Audio Video Interleave (AVI)
21, FASTA QUAL File
76, Perl program
1495, FASTA sequence file
15, Keyhole Markup Language (KML)
285, Rich Text Format (RTF)
490, R script
210, Phylogeny Inference Package (Phylip)
38, Hypertext Markup Language (HTML)
7, Moving Picture Experts Group (MPEG)
16, Portable Network Graphics (PNG)
209, JPEG Image
25, MP3 audio
2335, Zip archive
60, Python program
33, Mathematica Notebook
1339, Adobe Portable Document Format (PDF)
24, Postscript
59, UNIX Tar File Gzipped (TGZ)
10, MPEG-4 video
135, Bzip2 archive
13, Quicktime Video
4, Web Ontology Language (OWL)
22, Microsoft Excel Binary XML
89, Wave Audio Format
2, Graphics Interchange Format (GIF)
211, Roshal ARchive (RAR)
556, GZip archive
356, Newick tree file
596, Microsoft Word OpenXML
238, Tag Image File Format (TIFF)
9769, Plain Text
96, Tape Archive File (TAR)
2, Item-specific license agreed upon to submission
493, Microsoft Word 97-2007
267, Extensible Markup Language (XML)
1283, Nexus