Table 6.
Expected and observed error rates after filtering of aligned reads
| PhiX-Bv | PhiX-GA | |||||
|---|---|---|---|---|---|---|
| Expected (%) a | Observed (%) b | Percentage bases removed | Expected (%) a | Observed (%) b | Percentage bases removed | |
| No filter | 4.549 | 0.650 | 0.0 | 5.829 | 1.555 | 0.0 |
| ChF | 2.989 | 0.399 | 4.8 | 5.292 | 1.349 | 2.0 |
| C33 | 2.121 | 0.274 | 9.3 | 4.823 | 1.113 | 3.3 |
| B-tail | 0.166 | 0.130 | 7.0 | 0.194 | 0.309 | 9.0 |
| B-tail + ChF | 0.137 | 0.107 | 9.1 | 0.182 | 0.280 | 9.9 |
| B-tail + N | 0.159 | 0.130 | 7.2 | 0.187 | 0.310 | 9.5 |
| B-tail + C33 | 0.106 | 0.088 | 12.2 | 0.172 | 0.251 | 10.5 |
| B-tail + A30 | 0.114 | 0.092 | 11.3 | 0.172 | 0.262 | 10.5 |
| B-tail + ChF + C33 | 0.105 | 0.087 | 12.5 | 0.170 | 0.248 | 10.9 |
| B-tail + ChF + A30 | 0.113 | 0.091 | 11.6 | 0.170 | 0.257 | 10.8 |
aExpected error rate: average error probability of each base, assigned by Illumina as Q-scores. bObserved error rate: substitution error rate of aligned bases. ChF, Illumina chastity filter; B-tail, B-tail trimming; N, removal of reads with at least one uncalled base; C33, removal of reads that have less than two-thirds of Q ≥ 30 bases within the first half of the read; A30, removal of reads that have an average Q-score < 30 in the first 30% of the read.