Extended Data Figure 8: RNA-seq coverage of var genes in ring-stage wild-type 3D7-G7 clones (green line) and PfRNase II–FKBP H3 clones (red line).

Each plot contains the data of one var locus; that is, from 200 nt upstream of the start codon to 200 nt downstream of the stop codon. Accession numbers are shown above each plot. RNA-seq coverage on sense and antisense strands are shown in the upper and lower panels for each var gene, respectively. The y axis shows the RNA-seq read pileup coverage on a log₁₀ scale, normalized between samples by scaling with the inter-sample mean number of reads mapped to mRNA. The x axis shows the relative position of the var locus (left and right as the 5′ and 3′ ends of the locus, respectively), with the actual genomic range indicated in the axis label in the form [chromosome: strand: start position–end position]. The grey boxes on the x axis refer to the var exons. The repetitiveness of each relative position on the x axis is shown in an extra panel at the bottom, according to the colour scale at the right (from 1 to 20). a–d, Four representative var genes with different ups types and transcription statuses, as indicated on the top of each plot.