% coverage of SARS-CoV-2 whole genome with varying coverage thresholds.

Coverage percentage for the whole genome (WG) and for each gene/segment in all 3 time-points (tp1, tp2, tp3) for each of the 16 patients whose genome was sequenced. Five different coverages are shown, each considering a different threshold for depth of sequencing per position below which “no coverage” was recorded–depths of 1, 5 (used in the study), 10, 20 and 50. For each, the coefficient of determination (r2), the differences in coverage between tp1 and tp3 (Δtp1,3) and the paired T-test p.value of tp1 vs. tp3 (pval(tp1,3) are shown.
(XLSX)