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

Figure 4

Distribution of undetermined nucleotides length in 304 clinical samples. Undetermined nucleotides with read depths less than five are analyzed using sequence reads from 25% downsampled, 50% downsampled, or whole-FASTQ data (100%) obtained from single MiSeq runs for the 304 samples. Distributions of the lengths of the undetermined nucleotides are shown in the violin plots, while the box plots show the 1^st quantile, median, and 3^rd quantile values. The blue line shows the threshold of 1495 bp, which is 5% of the whole SARS-CoV-2 genome sequence.