1001 Genomes
A Catalog of Arabidopsis thaliana Genetic Variation
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CeBiTecRies2012 Nd-1

The genome of the Arabidopsis thaliana accession Niederzenz-1 (Nd-1, N1636) was sequenced using the Illumina short read platform and the 454 platform. Nd-1 is one parent of two reciprocal recombinant inbred lines (RILs) derived from the accessions C24 (N906) and Nd-1 generated in the lab of Thomas Altmann. These RILs have been used in the identification of metabolic and biomass QTL.

34167343 illumina short-reads and 3197257 454 reads were aligned against the genome sequence of the Arabidopsis reference accession Columbia (Col-0) genome (release TAIR10) to a depth of 19.4 respective 8.20197. Using the SHORE pipeline to identify variations of Nd-1 to TAIR-10 revealed 209700 SNPs and 18936 1-3 bp insertions for the 454 sequencing, as well as 503588 SNPs and 45353 1-3 bp insertions for the Illumina sequencing. Additional information about Copy Number Variations, copy variable positions, deletions, duplications and heterozygous positions is also provided.

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