Table 2 Sequence read classification and mapping to the SARS-CoV-2 genome
From: Evaluation of rRNA depletion methods for capturing the RNA virome from environmental surfaces
Sample | % Classified reads by Kraken2 | Distribution of reads classified | Identification of SARS-CoV-2 | ||||||
|---|---|---|---|---|---|---|---|---|---|
% Eukaryota | % Bacteria | % Viruses | No. of classified reads by Bracken | No. of mapped reads by BWA-MEM | Average depth of genome coverage | % Genome covered | % Reads mapped to 3'UTR | ||
TH | 95.1 | 19.9 | 79.8 | 0.061 | 0 | 81 | 0.1 | 0.1 | 100.0 |
TH-s100k | 95.7 | 19.8 | 79.7 | 0.319 | 12,693 | 51,083 | 240.2 | 100.0 | 1.6 |
TB | 95.0 | 88.8 | 11.0 | 0.076 | 0 | 84 | 0.1 | 0.1 | 100.0 |
TB-s100k | 94.6 | 89.1 | 9.5 | 1.412 | 65,368 | 55,076 | 260.6 | 100.0 | 1.1 |
TB-s10k | 94.4 | 88.8 | 11.0 | 0.201 | 5685 | 6236 | 28.2 | 98.0 | 3.7 |
TB-s1k | 94.6 | 89.3 | 10.6 | 0.087 | 421 | 941 | 2.7 | 43.3 | 37.5 |
TB-s0.1 k | 94.6 | 89.3 | 10.6 | 0.077 | 0 | 86 | 0.2 | 3.3 | 69.8 |
TB-s0.01 k | 94.6 | 89.3 | 10.6 | 0.081 | 0 | 72 | 0.1 | 0.1 | 100.0 |
NH | 87.3 | 29.6 | 70.4 | 0.054 | 0 | 1376 | 1.2 | 0.9 | 99.9 |
NB | 86.6 | 37.9 | 61.9 | 0.036 | 0 | 1437 | 1.2 | 0.2 | 94.0 |