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Table 3 Sequencing and variant calling errors of next-generation sequencing based on the data set of Sanger sequences of 13 AL8/78 BAC clones

From: Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

Error type Platform Overall error rate INDEL error rate Substitution error rate Insertion (%) Deletion (%) Substitution (%)
Sequencing error compared with Sanger sequences
Single read error Roche 454 GS-FLX Titanium 7.4 × 10-3 6.2 × 10-3 1.2 × 10-3 42.41 41.93 15.66
Consensus error Roche 454 GS-FLX Titanium 1.3 × 10-3 1.0 × 10-3 3.0 × 10-4 25.20 55.56 19.24
  Illumina Solexa 4.4 × 10-4 9.0 × 10-5 3.5 × 10-4 3.46 17.78 78.77
  AB SOLiD v2.0 4.3 × 10-4 2.5 × 10-4 1.8 × 10-4 10.69 47.58 41.73
Variant calling errors using Roche 454 sequence as reference
Consensus error Roche 454 GS-FLX Titanium 3.79 × 10-3 1.12 × 10-3 2.67 × 10-3 11.82 17.66 70.52
  Illumina Solexa 1.87 × 10-3 4.1 × 10-4 1.46 × 10-3 8.41 13.7 77.87
  AB SOLiD v2.0 5.9 × 10-4 2.7 × 10-4 3.2 × 10-4 21.71 24.67 53.62