Table 2 Sequencing metrics of selected food commodity and enrichment culture sample data generated using whole-metagenome shotgun and bait-capture approaches
Sample annotation | Sample type | Metagenomics sequencing method1 | Number of raw read (million) | Number of pass quality-filter read (million) | Number of read retained after dehosting (million) | Number of on-target read2 (million) | Non-host read percentage | On-target rate3 |
|---|---|---|---|---|---|---|---|---|
B 5 | Ground Beef | SH | 101.6 | 97.1 | 3.2 | 0.003 | 3.3% | 0.1% |
| Â | Â | T | 23.0 | 21.7 | 2.2 | 1.4 | 10.2% | 62.8% |
| Â | Ground Beef (enrichment) | SH | 66.1 | 62.2 | 49.8 | 0.1 | 80.0% | 0.1% |
| Â | Â | T | 19.6 | 17.8 | 17.7 | 8.7 | 99.6% | 48.9% |
B 3 | Ground Beef | SH | 86.7 | 82.8 | 7.1 | 0.01 | 8.6% | 0.2% |
| Â | Â | T | 16.6 | 16.0 | 2.8 | 1.6 | 17.4% | 58.5% |
| Â | Ground Beef (enrichment) | SH | 90.7 | 86.8 | 64.2 | 0.1 | 73.9% | 0.1% |
| Â | Â | T | 17.9 | 16.6 | 16.6 | 8.3 | 99.7% | 50.0% |
C 1 | Ground Chicken (enrichment) | SH | 84.6 | 81.3 | 66.0 | 0.2 | 81.1% | 0.3% |
| Â | Â | T | 25.4 | 23.6 | 22.5 | 13.6 | 95.1% | 60.5% |
P 3 | Ground Pork | SH | 100.8 | 96.2 | 50.4 | 0.03 | 52.4% | 0.1% |
| Â | Â | T | 28.0 | 25.2 | 18.0 | 8.6 | 71.4% | 47.6% |
| Â | Ground Pork (enrichment) | SH | 81.3 | 78.1 | 61.8 | 0.1 | 79.1% | 0.1% |
| Â | Â | T | 33.3 | 29.9 | 29.9 | 14.2 | 99.9% | 47.7% |
P 2 | Ground Pork (enrichment) | SH | 83.7 | 80.3 | 61.6 | 0.2 | 76.7% | 0.3% |
| Â | Â | T | 29.0 | 27.1 | 26.3 | 14.2 | 97.1% | 54.1% |
T 1 | Ground Turkey (enrichment) | SH | 70.0 | 58.3 | 58.2 | 0.1 | 99.9% | 0.1% |
| Â | Â | T | 31.4 | 29.4 | 29.3 | 16.8 | 99.7% | 57.5% |
AS 2 | Alfalfa sprouts | SH | 89.9 | 83.8 | 78.4 | 0.1 | 93.5% | 0.2% |
| Â | Â | T | 21.1 | 19.4 | 19.3 | 3.3 | 99.7% | 17.0% |
| Â | Alfalfa sprouts (enrichment) | SH | 82.1 | 65.8 | 65.8 | 0.1 | 100.0% | 0.2% |
| Â | Â | T | 29.4 | 26.9 | 26.9 | 15.0 | 100.0% | 56.0% |
MBS 1 | Mung bean sprouts | SH | 64.4 | 42.7 | 42.2 | 0.003 | 98.7% | 0.01% |
| Â | Â | T | 11.9 | 11.3 | 10.9 | 0.7 | 96.0% | 6.1% |
| Â | Mung bean sprouts (enrichment) | SH | 69.7 | 57.8 | 57.7 | 0.1 | 100.0% | 0.2% |
| Â | Â | T | 27.7 | 25.7 | 25.6 | 14.3 | 99.9% | 55.8% |
MBS 3 | Mung bean sprouts | SH | 63.2 | 52.5 | 49.6 | 0.01 | 94.4% | 0.02% |
| Â | Â | T | 12.6 | 12.2 | 10.8 | 1.6 | 88.4% | 14.4% |
| Â | Mung bean sprouts (enrichment) | SH | 69.6 | 56.7 | 56.7 | 0.1 | 100.0% | 0.1% |
| Â | Â | T | 32.4 | 29.8 | 29.7 | 16.6 | 99.9% | 56.0% |