Figure S3 - Ebola Virus Makona Intrahost Single-Nucleotide Variants (iSNVs). Related to Figure 2. (A) Distribution of the number of iSNVs per sample. Replicate sequencing and iSNV calling was completed for 150 samples, of which 65 had no iSNV calls. Mean iSNVs per sample (including samples without iSNVs) = 2.04; mean iSNVs per sample (among samples with iSNVs) = 3.6. (B) Sample coverage by date shows the temporal distribution of samples containing Ebola virus (EBOV) genomes with and without iSNV calls. As expected, samples with iSNV calls have generally higher coverage. (C) Intermediate-frequency variants can persist over time with minimal genetic drift, as demonstrated by the iSNV at position 18,911. The existence of intermediate frequency (10–30%) iSNVs in many different samples over time provides an argument against recurring mutations and may suggest a relatively wide transmission bottleneck between patients.