Extended Data Fig. 6: Quantification of deconvolution uncertainty in first detection of VOCs.

A-D. Bootstrap distributions of Freyja abundance estimates obtained by resampling read data from each sample corresponding to the first detection of that VOC in San Diego 1000 times with replacement. In all boxplots, box edges specify the first and third quartiles, solid line indicates the median, and whiskers delimit the maximum and minimum values within 1.5 times the inter-quartile range (IQR) of box edges. Outliers are denoted with individual markers. Two samplers were found to contain Delta on the same day. First detections were also confirmed using a VOC qPCR panel, as shown in Fig. 2 and Extended Data Table 3. 95% Confidence intervals for variant prevalence for each first detection event: A. Alpha: (0.232, 0.278), B. Delta: (0.336, 0.397), C. Delta: (0.676, 0.772), D. Omicron: (0.017, 0.021). E. Estimated proportion of Omicron sequences in clinical data. Omicron estimates tracked via S-gene target failure, SGTF (characteristic of Omicron lineage BA.1 and its descendants) qPCR assays for clinical samples in San Diego between November 27th, 2021-February 7th, 2022. First detection of Omicron through clinical genomic sequencing in San Diego was December 8th. Dotted line shows a rolling average with a window size of seven days.