Fig. 2

Comparison of sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows on SARS-CoV-2 isolate. a Percentage of the BEI WA1 isolate genome coverage at 10x at different subsampled read depths when sequenced with the indicated approach. b Percent of the BEI WA1 isolate genome coverage at 100x at different subsampled read depths when sequenced with the indicated approach. c Observed read depth for each of the expected amplicons for the BEI WA1 isolate amplified with the ARTIC v3 protocol at a subsampled read depth of 100,000 raw reads. d Observed read depth for each of the expected amplicons for the BEI WA1 isolate amplified with the tailed amplicon v1 (2 pool amplification) protocol at a subsampled read depth of 100,000 raw reads. e Observed read depth for each of the expected amplicons for the BEI WA1 isolate amplified with the tailed amplicon v2 protocol (4 pool amplification) at a subsampled read depth of 100,000 raw reads. f Variants detected for the BEI WA1 isolate at a read depth of up to 1,000,000 raw reads (or the maximum read depth for the sample if below 1,000,000 reads). The positions of all variants detected in this study are shown and bases where the sample matches the Wuhan-Hu-1 reference are shown in grey