(A) Number of within-host variants identified in each sample in each study, normalized to the length of the genome sequenced in each study. For each sample, we identified within-host variants that were present at a frequency of at least 3% at sites with minimum sequencing coverage of 200 reads. The center line of each box plot displays the median value; the box limits display upper and lower quartiles; and the whiskers extend up to 1.5 times the interquartile range. The number of samples in each study is listed in Supplementary Table 1. (B) Number of within-host variants identified in the 46 H3N2 samples when analyzing both members of each sequenced read pair, just read 1, or just read 2. Variants were called and data plotted as in (A).