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This article is part of a special issue on exome sequencing.

Open Access Highly Accessed Research

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome

Cyrille Saintenac, Dayou Jiang and Eduard D Akhunov*

Author Affiliations

Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506, USA

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Genome Biology 2011, 12:R88  doi:10.1186/gb-2011-12-9-r88

Published: 14 September 2011

Additional files

Additional file 1:

Depth of read coverage near exon junctions. The improvement of depth of read coverage near exon junctions was obtained by iterative alignment and trimming unaligned reads by one nucleotide after each step. Depth of coverage along FlcDNA1028 obtained without read trimming (black) and with read trimming (red). Median depths of coverage for the gene obtained without read trimming or with read trimming are represented, respectively, by black and red horizontal lines.

Format: PDF Size: 36KB Download file

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Additional file 2:

Capture assay statistics. This file provides the details of alignment statistics (length of reads, total number of reads generated, total number of reads aligned after and before trimming, percentage of target covered) obtained by mapping captured reads to the reference sequence.

Format: XLSX Size: 11KB Download file

Open Data

Additional file 3:

Median depth of coverage per base around GPC locus target boundaries. A set of 17 boundaries from the GPC locus having a depth of coverage less than 61× was selected. The average MDC was calculated for 17 off-target/on-target boundaries, including 500 bp upstream and downstream sequences.

Format: PDF Size: 64KB Download file

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Additional file 4:

Influence of bait properties on capture efficiency. MDC was calculated for 47,874 2× tiled baits. All baits with a MDC above 200 were removed from the analysis. MDC was plotted against different bait parameters values: GC, bait GC content; k-mers, median frequency of the bait sequence in the Chinese spring genome; PMFE, probe minimum folding energy; PHFE, probe hybridization free energy; HS, bait Hairpin score; DS, bait Dimer score; Tm1 and Tm2, melting temperatures 1 and 2. Details of parameter estimations are provided in the Materials and methods. Red curves represent the median of MDC per value of a parameter.

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Additional file 5:

Capture efficiency for 1× and 2× tiled regions of the GPC locus. (a) The cumulative distribution of MDC for 1× tiled (black lines) and 2× tiled regions (red lines). (b) The MDC per base along the bait for 1× tiled (black lines) and 2× tiled targets (red lines).

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Additional file 6:

Impact of GSSs and SNPs on coding sequence. Excel file showing the distribution of GSSs and SNPs between silent and replacement codon positions.

Format: XLS Size: 2.8MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 7:

List of discovered insertions and deletions. Excel file containing indels identified in the Ld and Td genomes.

Format: XLS Size: 31KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 8:

Validation of SNPs and GSSs by Sanger re-sequencing. Excel file containing a comparison of GSS and SNP sites between the sequence capture and Sanger sequencing datasets.

Format: XLS Size: 23KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 9:

Impact of mismatches between captured DNA and bait sequences on the median depth of coverage. The number of mismatches (includes SNPs and GSSs discovered between Ld and Td) between the captured DNA and bait sequences were plotted against the median depth of target coverage obtained for a region covered by bait.

Format: PDF Size: 1.2MB Download file

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Open Data

Additional file 10:

Annotation of CNV genes. Excel file listing CNV targets based on the CNV-seq analysis.

Format: XLS Size: 38KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 11:

FlcDNAs showing gene deletions in Ld or Td. Excel file listing five cases of PAV based on MDC and nine cases of homoelog-specific gene deletions based on the absence of a second variant at IVSs.

Format: XLS Size: 21KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 12:

Density of GSSs and SNP in coding and non-coding regions. Excel file showing the density of GSSs and SNP sites in 5' UTRs, exons and 3' UTRs.

Format: XLS Size: 20KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 13:

Distribution of SNPs along the wheat chromosomes. Excel file showing the location of each FlcDNA in the wheat deletion bin map [41] determined by comparing FlcDNA sequences with the sequences of wheat deletion bin mapped ESTs using the BLASTN program.

Format: XLS Size: 30KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 14:

Annotation of targeted genes. Excel file showing the annotation of genes included in the wheat sequence capture assay. Annotation was performed using the blast2GO program followed by assigning genes to functional groups defined by plant GO terms.

Format: XLS Size: 721KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data