Assessment of Alternate and Reference Allele proportions (AAF:RAF) Across 140 Infections.

Box and whisker plots illustrate the spread of RAF:AAF proportions for each mutation (median (bar); 25th and 75th percentiles (bottom and top of box, respectively); 10th and 90th percentiles (bottom and top whiskers, respectively)). The red dashed line at 50% identifies the demarcation at which the alternate allele is recognized and reported as the conventional consensus nucleotide that characterizes the infecting virus. These 75 mutations were chosen for further analysis because they all showed evidence of biallelic states at greater than the 5% background threshold and were shared in more than 10 infections (blue dashed line). Among these varying positions, Illumina sequence reads for 30 mutations did not reach an AAF:RAF >50% for any of the 140 infections (shaded gray in aligned table); 45 positions exceeded the RAF:AAF 50% threshold for a portion of the 140 infections and would therefore have contributed to characterization of the infecting viral strain. The accompanying table enumerates the number of samples with AAF between 5 and 95%, 50%. Overall, among the 5,390 alternate alleles detected at a frequency >5%, just 975 (18%) were observed at >50% frequency necessary to be reported in consensus sequence. Nucleotide positions characterized by biallelic iSNVs in our VA study population and the samples queried in the sequence read archive (SRA) (S1 Fig) are designated by a green dot.