Overall taxonomic composition of RNA-seq reads and numbers of viral reads by respiratory virus. (A) Fractional abundance of reads binned as human, human mRNA (referred to as “mRNA”), any bacterial sequence (referred to as “bacterial”), bacterial 16S only (referred to as “16S”), viral, phage, any fungal sequence (referred to as “fungal”), fungal ITS only (referred to as “ITS”), ambiguous, and unknown is shown as median and interquartile range (box plots) and as violin plots. Only reads identified as viral (red, median ∼1:10−4 reads) were used for this analysis. (B) Viral read counts differed across 5 orders of magnitude. Viruses not targeted by the RVP are shown in red. ADV, adenovirus; HMPV, human metapneumovirus; IAV, influenza A virus; PIV, parainfluenza virus; HRV, human rhinovirus; RSV, respiratory syncytial virus; HCoV, human coronavirus; CMV, cytomegalovirus; HBoV, human bocavirus; EV, enterovirus; MV, measles virus; ITS, internal transcribed spacer.