1001 Genomes
A Catalog of Arabidopsis thaliana Genetic Variation
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JGIHeazlewood2008 Bay-0 and Shahdara

These data were recently realigned against the Arabidopsis Col-0 genome release TAIR10 which resulted in an average depth of 26.29x (Bay-0) and 30.22x (Sha). Analysis was performed using maq-0.7.1 and resulted in 339,255 SNPs in Bay-0 and 220,055 SNPs in Sha. Available data files now include SNPs (SNVs), indels, regions of structural variation, possible deletions and raw data in bam format.

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The genomes of two inbred Arabidopsis accessions Bayreuth (Bay-0: CS22633) and Shahdara (Sha: CS22652) were sequenced using the Illumina short read platform and aligned against the genome sequence of the Arabidopsis reference accession Columbia (Col-0) genome release TAIR8. A total of 73,018,266 reads were aligned for Bay-0 at an average depth of 17.5x while 85,576,951 reads were aligned for Sha at an average read depth of 20.4x. Variations were initially identified using maq software and revealed about 350,000 variations in Bay-0 and approximately 450,000 variations in Sha when compared to the reference sequence Col-0 (TAIR8). To improve the overall confidence of variant calls data were also analyzed using SHOREmap. The consensus of variations between the two techniques was over 90% for both Bay-0 (317,108 SNPs) and Sha (402,711 SNPs). Data files containing these overlapping SNP calls are available as tab delimited files.

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