Oryza sativa japonica genome assembly

This directory contains annotation and sequence data files from rice genome assembly Os-Nipponbare-Reference-IRGSP-1.0 released October 2011. Files are formatted for visualization in Integrated Genome Browser (IGB).

Files include:

• 2bit file - sequence file in two-bit format, created using faToTwoBit. When users click Load Sequence buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version. To obtain a copy of faToTwoBit, visit http://hgdownload.cse.ucsc.edu/admin/exe/.
• annots.xml - meta-data file that lists available data sets and specifies how they will look once loaded into Integrated Genome Browser.
• genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file. To obtain a copy of twoBitInfo, visit http://hgdownload.cse.ucsc.edu/admin/exe/
• reference gene model annotations in bed or bed detail format, compressed using bgzip and indexed using tabix (See: Tabix: fast retrieval of sequence features from generic TAB-delimited files and http://genome.ucsc.edu/FAQ/FAQformat.html.)

Note: Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB.

Gene model annotation files include:

• O_sativa_japonica_Oct_2011.bed.gz - RGAP/MSU7 gene models, from the Rice Genome Annotation Project at MSU.
• IRGSP-1.0_representative_2013-04-24.bed.gz - From the Rice Annotation Project Database RAP-Db.

For more information about quickload, visit bioviz.org/igb and visit the on-line, searchable IGB User's Guide.

	Name	Last modified	Size	Description
	Parent Directory		-
	genome.txt	2023-06-16 14:10	221	Chromosome lengths and assembly information
	annots.xml	2023-06-16 14:10	583	Annotation and data file list
	O_sativa_japonica_Oct_2011.bed.gz.tbi	2023-06-16 14:10	228K	Tabix index file
	O_sativa_japonica_Oct_2011.bed.gz	2023-06-16 14:10	2.8M	Annotation or junction file
	O_sativa_japonica_Oct_2011.2bit	2023-06-16 14:10	89M	Sequence data in blat 2bit format
	IRGSP-1.0_representative_2013-04-24.bed.gz.tbi	2023-06-16 14:10	170K	Tabix index file
	IRGSP-1.0_representative_2013-04-24.bed.gz	2023-06-16 14:10	2.2M	Annotation or junction file