Malus domestica (apple) June 2017 genome assembly

This directory contains annotation and sequence data files from the GDDH13 Version 1.1 apple genome released in June 2017. 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.)
• sub-directories with additional data, including mRNA and EST alignments, RNA-Seq data sets, etc.

Note: Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB. Gene model annotation files use BED-detail format, which is the same as BED12 but contains two additional fields: field 13 contains the locus identifier and field 14 contains descriptive text.

	Name	Last modified	Size	Description
	Parent Directory		-
	M_domestica_Borkh_Jun_2017.2bit	2023-06-16 13:42	169M	Sequence data in blat 2bit format
	M_domestica_Borkh_Jun_2017.bed.gz	2023-06-16 13:42	2.5M	Annotation or junction file
	M_domestica_Borkh_Jun_2017.bed.gz.tbi	2023-06-16 13:42	260K	Tabix index file
	annots.xml	2023-06-16 13:42	359	Annotation and data file list
	genome.txt	2023-06-16 13:42	270	Chromosome lengths and assembly information