Differential gene expression. Differential counts of reads mapping to A. apis gene models between culture types, with positive values indicating higher abundance in host infection relative to axenic culture. A) Differential counts of reads, normalized by both total reads mapped and transcript length (RPKM), between host infection and axenic culture is plotted on a log2 scale on the vertical axis. Values are plotted as a function of gene length in nucleotides because the variance in RPKM is greater for shorter genes. Black points are greater than two standard deviations from the mean RPKM for a sliding window of 500 genes, ranked by length. B) Differential counts of reads normalized for total mapped reads in each library but not for length of predicted transcript. Log2 differential is on the horizontal axis and significance by Fisher’s Exact Test with multiple test correction is on the vertical axis. Colors indicate progressive ranges of probability of the null hypothesis (equal abundance in both samples), plotted as the -log10 (P-value) for clarity.