Bay-0 and Shakdara polymorphisms (JGI)

The entire genome of strain A. thaliana Bay-0 and Shakdara was sequenced using the Illumina GA II Short Read platform. These sequences were aligned and variants identified using MAQ (Mapping short DNA sequencing reads and calling variants using mapping quality scores. Li H, Ruan J, Durbin R; Genome Res. 2008 Aug 19. [Epub ahead of print] MAQ version 0.6.5 at default settings)(reference Col-0 tair 8 TBD: March/14/2008).
Bay-0 : A total of 73,018,266 reads were aligned generating an average depth of 17.5x at unique regions of the genome and 343,295 potential variants were identified. Of these variants, 317,108 were also independently identified by a second program ShoRe (Detlef Weigel unpublished data) and are the putative variants presented in this track.
Shakdara : A total of 85,576,951 reads were aligned generating an average depth of 20.4x at unique regions of the genome and 435,130 potential variants were identified. Of these variants, 402,711 were also independently identified by a second program ShoRe (Detlef Weigel unpublished data) and are the putative variants presented in this track.