Table 2.
Sensitivity of intergenus predictions for various QC metrics by species (averaged over mixing ratio and contaminant species). Values are the number of contamination predictions (QC metrics above or below thresholds) [TP] divided by number of contaminated samples [P]. Good predictions (>0.8 accuracy) are colored in light blue, sufficient predictions (>0.2) in orange and insufficient predictions in white. Perfect predictions are shown in bold.
| Predictor | Campylobacter spp. | E. coli | L. monocytogenes | S. enterica |
|---|---|---|---|---|
| ConFindr cgMLST | 0.98 | 1.00 | 1.00 | 1.00 |
| ConFindr rMLST | 1.00 | 1.00 | 0.99 | 1.00 |
| # contigs | 0.79 | 0.90 | 0.60 | 0.88 |
| Dupl. BUSCO | 0.55 | 0.89 | 0.56 | 0.82 |
| Duplication ratio | 0.00 | 0.40 | 0.00 | 0.41 |
| GC content | 0.35 | 0.00 | 0.35 | 0.40 |
| Kraken2 contigs | 0.79 | 0.89 | 0.60 | 0.80 |
| Kraken2 reads | 1.00 | 1.00 | 1.00 | 1.00 |
| Duplicated mlst | 0.00 | 0.21 | 0.00 | 0.11 |
| N50 | 0.38 | 0.76 | 0.40 | 0.42 |
| Unique BUSCOs | 0.41 | 0.82 | 0.42 | 0.75 |
| assembly length | 0.64 | 0.85 | 0.59 | 0.80 |