Transcript 5' ends of psbB , petF , nrrA , psbAI , atp1 , and rbcL. RNA-seq coverage at each base along a gene's ORF and UTR are mapped below the gene. RNA-seq reads for psbB, petF, nrrA, and psbAI show clear 5' ends (characterized by an abrupt drop to 0 coverage) at -328, -100, -27, and -65, respectively, which correspond with published results obtained with other methods. However, atp1 and rbcL show trailing reads without a complete break upstream of the mapped 5' ends at -221 and -414, respectively, indicating that transcription originates further upstream. RNA abundance along a transcript varies with message stability, often resulting in higher coverage at the 5' end of messages. Scales on left are reads per base position. All data shown are from the 0 h time point with the exception of nrrA, which is from the 21 h time point. Green and blue, ORF orientation and RNA-seq reads to the right and left, respectively.