| |
Expected error ratea(percentage of bases discarded)
|
|---|
|
Filter
|
Bv + PhiX
|
At + PhiX
|
PhiX-GAIIx
|
|---|
|
No filter
|
7.093 (0.0%)
|
10.619 (0.0%)
|
16.434 (0.0%)
|
|
ChF
|
2.583 (10.2%)
|
4.819 (12.7%)
|
7.360 (17.8%)
|
|
B-tail
|
0.163 (11.0%)
|
0.205 (16.6%)
|
0.229 (25.8%)
|
|
N
|
5.943 (2.5%)
|
9.688 (2.3%)
|
8.601 (15.6%)
|
|
C33
|
1.521 (14.3%)
|
2.907 (17.7%)
|
5.207 (21.7%)
|
|
A30
|
1.802 (12.7%)
|
3.586 (15.5%)
|
5.457 (21.3%)
|
|
B-tail + N
|
0.141 (11.4%)
|
0.187 (17.0%)
|
0.206 (26.8%)
|
|
B-tail + ChF
|
0.118 (13.8%)
|
0.161 (19.2%)
|
0.204 (27.2%)
|
|
B-tail + ChF + C33
|
0.083 (16.9%)
|
0.127 (22.1%)
|
0.174 (28.3%)
|
|
B-tail + ChF + A30
|
0.093 (15.8%)
|
0.139 (21.0%)
|
0.176 (28.2%)
|
|
B-tail + ChF + N + C33
|
0.077 (17.1%)
|
0.125 (22.2%)
|
0.168 (28.9%)
|
|
B-tail + ChF + N + A30
|
0.085 (16.0%)
|
0.136 (21.1%)
|
0.171 (28.6%)
|
-
aExpected error rate: average error probability of each base assigned by Illumina as quality scores. No filter, raw data prior to filtering; ChF, Illumina chastity filter; B-tail, B-tail trimming; N, removal of reads with at least one uncalled base; C33, removal of reads having less than two-thirds of bases with Q ≥ 30 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. Note that some quality filters discard partially the same reads (for instance, the chastity filter and the removal of reads containing at least one uncalled base).
