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Table 6 Expected and observed error rates after filtering of aligned reads

From: Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

  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
  1. 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.