Figure 2

Classification of 50-bp sequencing reads and effect of increasing sequencing depth. (A) The total number of 50-bp sequencing reads, matching the paired-end analysis criterion that both reads could be aligned to the M. bovis BCG genome, were assigned to four different categories (protein-coding RNA, ribosomal RNA, small RNA, and other). The total of the reads for each sample represents the number of reads aligning to the M. bovis BCG genome. (B) Simulation of the relation between the number of differentially expressed M. bovis BCG genes and sequencing depth. Random subsets of reads were selected from EGB, IF1ER and IF2ER and the mean number (n = 5) of reliably identified differentially expressed genes (FDR < 0.05) and the standard deviation (error bars) are given for various sequencing depths. Note that the ratio of a random set to the total set approaches 1 as the size of the random set increases. Therefore, the random samples become more similar to each other and the standard deviation decreases. For reasons of completeness, we have included a standard deviation for every point. (C) Classification of the relative number of 50-bp paired-end sequencing reads aligning to the M. bovis BCG genome. The legend is the same as in (A).