Table 2.
Alignment comparison of corresponding uncorrected and corrected reads against the reference genome
| Corrected (Abundance (counts/kb)) | Introduced (Abundance (counts/kb)) | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Platform (Run) | Total | Mismatches | Insertions | Deletions | Total | Mismatches | Insertions | Deletions | |
| GS Junior (1) | 81% | 76% (0.33) | 82% (2.28) | 81% (0.81) | 4% | 11% (0.048) | 2% (0.065) | 6% (0.063) | |
| GS Junior (2) | 85% | 79% (0.24) | 86% (2.23) | 83% (0.76) | 4% | 15% (0.044) | 2% (0.059) | 6% (0.050) | |
| PGM (1) | 88% | 82% (1.68) | 91% (7.67) | 86% (7.10) | 3% | 2% (0.046) | 2% (0.16) | 5% (0.44) | |
| PGM (2) | 86% | 80% (1.72) | 90% (7.47) | 84% (7.70) | 4% | 2% (0.052) | 2% (0.16) | 6% (0.52) | |
| MiSeq | 94% | 95% (0.85) | 10% (0.0015) | 78% (0.007) | 1% | 1% (0.010) | 4% (0.0007) | 8% (0.0007) | |
All reads are sequenced from the same O104:H4 E. coli isolate. Corresponding uncorrected and corrected reads are aligned to the reference genome using SMALT. Incomparable alignments are removed. Corrected errors reflect alignment errors which are found in uncorrected reads but not in corrected reads. Similarly, introduced errors are a consequence of alignment errors found in corrected reads but not in uncorrected reads.