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. 2022 Oct 7;25(11):105310. doi: 10.1016/j.isci.2022.105310

Figure 2.

Figure 2

Analysis of alignment of data to SARS-CoV-2 genome

(A) Schematic overview of the SARS-CoV-2 genome.

(B) Comparison of SARS-CoV-2 genome coverage as determined using Bedtools genomecov. Data were partitioned based on viral load of PCR-positive samples (High, Med, Low), and the PCR negative sequencing positive samples (PCR-ve). % Coverage was calculated for each sample as ((number reads in SARS-CoV-2 genome position) / (total number of SARS-CoV-2 aligned reads))∗100.

(C) Comparison of SARS-CoV-2 transcript coverage as determined using RSeQC geneBody coverage. Data were partitioned based on viral load of PCR-positive samples (High, Med, Low), and the PCR negative sequencing positive samples (PCR-ve). % Coverage was calculated for each sample as ((number reads in SARS-CoV-2 gene body percentile) / (total number of SARS-CoV-2 aligned reads))∗100.

(D) Expression of SARS-CoV-2 genes in RNA sequencing data. Read counts were converted to TPM and plotted for each PCR negative sequencing positive sample.