Figure 1

Accumulation of 36-bp reads to cover whole transcripts. (a) Cumulative coverage of rice genome and annotated region. Data from nine technical replicates of reads from roots after salinity stress were accumulated. Cumulative coverage was calculated by using reads uniquely mapped on the rice genome (black) or the RAP2 annotated region (white). As the number of reads increased, the cumulative coverage approached a plateau. (b) Robustness of the measurement of transcripts in four different expression classes. Saturation of sequencing was estimated on the basis of the fraction of RAP2 genes supported by FL-cDNA sequences that had reached their final RPKM (reads per kilobase of exon model per million mapped reads) [16]. Vertical axis indicates the fraction of genes for which the RPKM was within 5% of the final value, and horizontal axis indicates the cumulative number of uniquely mapped reads. The fraction of highly expressed genes was almost unchanged, whereas those of genes with relatively low expression converged slowly. N indicates the number of transcripts in each of the four classes.