COVID-19 Whole-Genome Resequencing with Redundant Tiling PCR and Subtract-Based Amplicon Normalization Successfully Characterized SARS-CoV-2 Variants in Clinical Specimens

Figure 2

Amplicon bias among four samples is largely consistent but influenced by SNVs on the primer annealing site. (a) Comparison of normalized counts for each amplicon from NIID and three Bangladesh clinical samples (BGD1, 2, and 3). Log10-transformed amplicon counts normalized from 100,000 mapped reads are shown. Pairwise comparisons with Pearson’s correlation values are shown in the upper right quadrant. (b) Read depths for each sample in the region spanning region_002 (left black line), region_003 (middle red line), and region_004 (right black line) are shown. The SARS-CoV-2 sequence from BGD3 had a mutation on the reverse primer for region_003. Read depths were normalized from 100,000 mapped reads.

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