Fig. 3

Characterization of cDNA reads of mixed blood stages of Plasmodium y. nigeriensis N67 and N67C. mRNAs were extracted from blood samples with mixed stages of parasites collected from 10 mice, five infected with either N67 or N67C parasites, and were processed for directional RNA-Seq as described in the Methods. A and B Representative images of blood smears from mice infected with N67 and N67C day 4 post-infection. C Mean quality scores of cDNA reads estimated using FASTQC [26]. Mean Phred quality score plot against each base call position. D Percentages of reads mapped to a gene or multiple gene families using RSEM package [27]. E Percentages of reads mapped to coding, intronic, intergenic, untranslated regions (UTR), or not aligned using Picard [25]. F Percentages of reads from sense and antisense transcripts predicted using RSeQC [24]