Open Access Highly Accessed Methodology article

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

Frank M You12, Naxin Huo12, Karin R Deal1, Yong Q Gu2, Ming-Cheng Luo1, Patrick E McGuire1, Jan Dvorak1* and Olin D Anderson2*

Author Affiliations

1 Department of Plant Sciences, University of California, Davis, CA, 95616, USA

2 Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA

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BMC Genomics 2011, 12:59  doi:10.1186/1471-2164-12-59

Published: 25 January 2011

Additional files

Additional file 1:

Supplementary tables and figures. The file contains Table S1, Figure S1, S2 and S3. Table S1 lists all pipeline scripts for annotation-based SNP discovery. Figure S1 shows the relationship of percentage of the same SNPs identified by two NGS platforms with overlapping percentage of reads generated between two NGS platforms. Figure S2 presents gene coverage of NGS reads with different genome coverage of NGS reads and with different sequencing platforms. Figure S3 depicts the relationship of the number of detected SNPs with the number of genotypes used for SNP discovery.

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