This directory contains gzip compressed GVF (Genome Variation Format) files: oryza_glumipatula.gvf.gz All germline variations from the current Ensembl release for this species oryza_glumipatula_structural_variations.gvf.gz All structural variations (if available for this species) oryza_glumipatula_failed.gvf.gz Any variations that have been failed by the Ensembl QC checks oryza_glumipatula_incl_consequences.gvf.gz All consequences of the variations on the Ensembl transcriptome, as called by the variation consequence pipeline If available for this species, the file includes information on: - ancestral_allele - evidence - clinical_significance - global minor allele, frequency and count Incl_consequences files include sift (if available for this species) and polyphen (human only) predictions. 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: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gvf.md We use the sum command for calculating checksums. Questions about these files can be addressed to the Ensembl helpdesk: helpdesk@ensembl.org, or to the developer's mailing list: dev@ensembl.org. ----- Example content from the human germline GVF dump is shown below: ##gff-version 3 ##gvf-version 1.07 ##file-date 2014-07-13 ##genome-build ensembl GRCh38 ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/so.obo?revision=1.283 ##data-source Source=ensembl;version=76;url=http://e76.ensembl.org/Homo_sapiens ##file-version 76 ##sequence-region 8 1 145138636 8 dbSNP SNV 60059 60059 . + . ID=1;Variant_seq=T;Dbxref=dbSNP_138:rs371829072;Reference_seq=C 8 dbSNP SNV 60211 60211 . + . ID=2;Variant_seq=T;Dbxref=dbSNP_138:rs376064598;Reference_seq=G 8 dbSNP SNV 60220 60220 . + . ID=3;Variant_seq=A;Dbxref=dbSNP_138:rs368575943;Reference_seq=G 8 dbSNP SNV 60251 60251 . + . ID=4;Variant_seq=T;Dbxref=dbSNP_138:rs372357503;Reference_seq=C 8 dbSNP SNV 60288 60288 . + . ID=5;Variant_seq=G;Dbxref=dbSNP_138:rs375561901;Reference_seq=C 8 dbSNP SNV 60290 60290 . + . ID=6;Variant_seq=C;evidence_values=Multiple_observations;Dbxref=dbSNP_138:rs200947342;Reference_seq=A 8 dbSNP SNV 60323 60323 . + . ID=7;Variant_seq=G;Dbxref=dbSNP_138:rs199540500;Reference_seq=C 8 dbSNP SNV 60341 60341 . + . ID=8;Variant_seq=G;evidence_values=Multiple_observations;Dbxref=dbSNP_138:rs201908809;Reference_seq=C 8 dbSNP SNV 60346 60346 . + . ID=9;Variant_seq=G;Dbxref=dbSNP_138:rs78893626;Reference_seq=A