A quarter of household pairs share more iSNVs than random expected by chance.

a. We modeled the probability that 2 consensus genomes will share x mutations as Poisson-distributed with lambda equal to the number of mutations expected to accumulate in the SARS-CoV-2 genome over 5.8 days [37] given a substitution rate of 1.10 x 10−3 substitutions per site per year [1]. Exploration of how these probabilities change using a range of plausible serial intervals and substitution rates is shown in S8 Fig. The vast majority of genomes that are separated by one serial interval are expected to differ by ≤2 consensus mutations. b. The proportion of random pairs (grey) and putative household transmission pairs (purple) is shown on the y-axis vs. the proportion of iSNVs shared. The dotted line indicates the 95th percentile among the random pairs. Household pairs that share a greater proportion of iSNVs than 95% of random pairs (i.e., are plotted to the right of the dotted line) are considered statistically significant at p = 0.05. iSNVs had to be present at a frequency of ≥3% to be considered in this analysis. c. We assessed the impact of household membership, clade membership, phylogenetic divergence, and geographic distance on the proportion of iSNVs shared between each pair of samples in our dataset. The mean of each estimated coefficient in the combined linear regression model including all predictors is shown on the x-axis, with lines of spread indicating the range of the estimated 95% highest posterior density interval (HPDI).