Table 3.
Comparison of the most important whole-genome sequencing quality parameters in Illumina, MinION amplicon, and MinION direct.
| Sample | Coverage (%) | Mean read quality (Phred Quality Score) | Estimated contig length N50 (bp) | Identity levels (%) | Assembled reads (%) | Depth (average log10 transformed) | Number of total reads | Total bases | Final error rate (%; substitution and deletion) |
|---|---|---|---|---|---|---|---|---|---|
| Illumina | |||||||||
| 1 | 99 | 35.3 | 2,742 | 99 | 93 | 4.3 | 5,268,103 | 1.6 Gb | 0.15 |
| 2 | 99 | 35.2 | 2,176 | 99 | 92 | 3.8 | 10,667,810 | 4.3 Gb | 0.12 |
| 3 | 99 | 35.5 | 3,862 | 99 | 95 | 2.9 | 6,959,105 | 2.1 Gb | 0.11 |
| 4 | 99 | 33.4 | 2,432 | 99 | 89 | 3.9 | 6,030,472 | 1.9 Gb | 0.18 |
| MinION amplicon | |||||||||
| 1 | 99 | 25 | 3,176 | 99 | 92 | 4.0 | 292,000 | 1.2 Gb | 2.02 |
| 2 | 99 | 22 | 2,872 | 99 | 92 | 3.2 | 220,000 | 980 Mb | 1.86 |
| 3 | 99 | 23 | 4,152 | 98 | 92 | 2.4 | 288,000 | 1.1 Gb | 1.62 |
| 4 | 99 | 22 | 2,766 | 98 | 88 | 3.3 | 292,000 | 1.2 Gb | 2.28 |
| MinION direct | |||||||||
| 1 | 52 | 19 | 800 | 76 | 42 | 1.0 | 32,000 | 80 Mb | ≥4 |
| 2 | 64 | 18 | 755 | 85 | 38 | 0.8 | 52,000 | 122 Mb | ≥4 |
| 3 | 75 | 20 | 900 | 71 | 35 | 0.5 | 68,000 | 151 Mb | ≥4 |
| 4 | 49 | 20 | 920 | 82 | 36 | 0.8 | 48,000 | 98 Mb | ≥4 |
Gb, Gigabyte; Mb, Megabyte.