This directory contains a gzip compressed GVF (Genome Variation Format) file
containing all germline variations from the current Ensembl release for this 
species, named Puccinia_graminisug99.gvf.gz. If this species has any structural 
variation data this is provided in a file named 
Puccinia_graminisug99_structural_variations.gvf.gz

Any variations that have been failed by the Ensembl QC checks will be included
in a file called Puccinia_graminisug99_failed.gvf.gz.

A file including the consequences of the variations on the Ensembl transcriptome, 
as called by the variation consequence pipeline, can be found in a file called 
Puccinia_graminisug99_incl_consequences.gvf.gz.

For human we also provide a file containing all somatic mutations in the
database, files with germline variations observed in the Watson and Venter 
genomes along with their genotypes, and files containing allele frequencies
from several of the HapMap and 1000 genomes pilot study populations.

Please note that depending on the amount of variation data available for this 
species the uncompressed file may be very large (e.g. the entire germline file 
for human is ~3GB and the file including consequences is ~9GB).

The data contained in these files is presented in GVF format, this is a
simple tab-delimited format derived from GFF3 which shows the location of 
each variant along with the reference and variant sequences, an identifier 
for the source of the data (typically a dbSNP rsID), and other relevant 
information (e.g. genotypes, allele frequencies, the predicted effect of 
this variant on a transcript), a short example is presented below. For 
more details about GVF please refer to:

Reese, M.G. et al. A standard variation file format for human genome sequences.
Genome Biology. 2010;11(8):R88 PMID: 20796305

and:

http://www.sequenceontology.org/gvf.html

Questions about these files can be addressed to the Ensembl helpdesk: 
http://www.ensembl.org/Help/Contact, or to the developer's mailing list: http://lists.ensembl.org/mailman/listinfo/dev.

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Example content from the human germline GVF dump is shown below:

##gff-version 3
##file-date 2011-01-31
##genome-build ensembl GRCh37
##gvf-version 1.05
##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/so.obo?revision=1.283
##data-source Source=ensembl;version=61;url=http://e61.ensembl.org/Homo_sapiens
##file-version 61
##sequence-region 11 1 135006516
11	dbSNP	SNV	61554	61554	.	+	.	ID=1;Variant_seq=C;Dbxref=dbSNP_132:rs77355429;Reference_seq=A
11	dbSNP	SNV	61645	61645	.	+	.	ID=2;Variant_seq=C;Dbxref=dbSNP_132:rs61869610;Reference_seq=G
11	dbSNP	SNV	61868	61868	.	+	.	ID=3;Variant_seq=A;Dbxref=dbSNP_132:rs365553;Reference_seq=G
11	dbSNP	SNV	67521	67521	.	+	.	ID=4;Variant_seq=G;Dbxref=dbSNP_132:rs76077193;Reference_seq=A
11	dbSNP	SNV	70073	70073	.	+	.	ID=5;Variant_seq=C;Dbxref=dbSNP_132:rs1099703;Reference_seq=T
11	dbSNP	SNV	70113	70113	.	+	.	ID=6;Variant_seq=T;Dbxref=dbSNP_132:rs76956518;Reference_seq=C
11	dbSNP	SNV	70133	70133	.	+	.	ID=7;Variant_seq=T;Dbxref=dbSNP_132:rs112541484;Reference_seq=C
11	dbSNP	SNV	70135	70135	.	-	.	ID=8;Variant_seq=A;Dbxref=dbSNP_132:rs4120101;Reference_seq=C
11	dbSNP	SNV	70146	70146	.	-	.	ID=9;Variant_seq=C;Dbxref=dbSNP_132:rs4120100;Reference_seq=A