################################################################### # Data release of the Nd-1 Arabidopsis thaliana. # date: 2012_06_01 ################################################################### Data analysis description: The Nd-1 genome was analyzed using the short read pipeline SHORE (Ossowski et al, Genome Res, 2008). The data, consisting of 400 bp 454 reads was annotated against the TAIR10 assembly. The results consist of 10 files which are described in the following: CNV.txt.gz copy_variable_position.txt.gz deletion.txt.gz duplication.txt.gz heterozygous_position.txt.gz homozygous_snp.txt.gz insertion.txt.gz reference.txt.gz unsequenced.txt.gz For a detailed description of the file content, please have a look at: http://sourceforge.net/apps/mediawiki/shore/index.php?title=Shore_consensus Quality values are in Illumina format. They range from 1 to 40, where 40 specifies highest quality. ################################################################### # File content description. ################################################################### 1) Quality Data (filtered_reference, filtered_variant and insertion) reference.txt.gz Positions that equal the reference base. homozygous_snp.txt.gz Positions and annotation of SNPs (single nucleotide polymorphisms) detected through short read alignments. insertion.txt.gz 1-3 bp length insertions annotated through the short read alignments. deletions.txt.gz 1-16 bp length deletions annotated through the short read alignments. copy_variable_position.txt.gz Positions indicating duplications. CNV.txt.gz Regions of putative copy number variations, predicted by a strong skew in coverage and the occurance of copy variable positions. duplication.txt.gz Duplications are called similar to copy number variations, but with higher requirements and are thus more reliable. heterozygous_position.txt.gz This file includes minor alleles of SNPs and indels. unsequenced.txt.gz Regions that are uncovered by reads. ################################################################### # File format description ################################################################### CNV.txt.gz copy_variable_position.txt.gz deletion.txt.gz duplication.txt.gz heterozygous_position.txt.gz homozygous_snp.txt.gz insertion.txt.gz reference.txt.gz unsequenced.txt.gz ------------------------------------------------------------------- Bielefeld, Germany, 2012 Questions? David Ries