Additional file 3.

Distribution of RNA-Seq sequences within the grapevine genome. (A) Proportions of reads mapping to unique locations (unique reads, yellow), reads mapping to multiple locations with 2–100 matches (multi-reads, red), and reads not mapping or ambiguously mapping to more than 100 locations (unused reads, white) to the grapevine genome. The mean number of sequenced reads and standard errors for three biological replicates are presented for each treatment. Percentages (%) are calculated with respect to the total filtered reads. Unique reads and multi-reads were used for evaluating gene expression. (B) Proportions of reads mapping to grapevine genes (green) and to intergenic regions (red) of the grapevine genome. The mean number of sequenced reads and standard errors for three biological replicates are presented for each treatment. Percentages (%) are calculated with respect to the total mapping reads. Grapevine treatments: control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v) plants.

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Perazzolli et al. BMC Genomics 2012 13:660   doi:10.1186/1471-2164-13-660