Table 2.
Quantity and proportion of sequence reads with a positive BLASTN hit against the model organism groups used in the virus discovery metagenomic dataset, comparing the effect of different virus enrichment methods.
| Treatment | Total number of sequence readsa | Metazoa |
Enterobacteriaceae |
Adenovirus |
Influenza |
Enterovirus |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| BLASTN hits | % total | BLASTN hits | % total | BLASTN hits | % total | BLASTN hits | % total | BLASTN hits | % total | ||
| No treatment | 1,980,878 | 39,481 | 1.99% | 1,523,514 | 76.9% | 40 | 0.002% | 20 | 0.001% | 3,221 | 0.16% |
| Centrifuge | 2,010,717 | 48,719 | 2.42% | 1,486,125 | 73.9% | 0 | 0.000% | 77 | 0.004% | 14,805 | 0.74% |
| Filtration | 1,941,626 | 65,746 | 3.39% | 1,334,433 | 68.7% | 6 | 0.000% | 110 | 0.006% | 22,731 | 1.17% |
| Nuclease | 1,821,828 | 5,148 | 0.28% | 1,421,268 | 78.0% | 17 | 0.001% | 14 | 0.001% | 2,532 | 0.14% |
| 2-step treatmentb | 1,730,569 | 53,421 | 3.09% | 1,199,232 | 69.3% | 14 | 0.001% | 57 | 0.003% | 18,712 | 1.08% |
| 3-step treatmentb | 1,417,803 | 26,856 | 1.89% | 857,873 | 60.5% | 16 | 0.001% | 161 | 0.011% | 67,227 | 4.74% |
a
Combined total number of sequence reads for two independent physical replicates which were also run on different Illumina MiSeq flowcells. This figure represents the collapsed sequencing data, therefore redundant reads are not represented more than once.
b
Serial applications of treatment methods. The 2-step method consisted of centrifugation then filtration. The 3-step method consisted of centrifugation, filtration then nuclease-treatment.